I have used the original disks and reference materials in constructing this chronology. I have been especially careful when reviewing the information presented in Apple Knowledge Base article 15582, Macintosh: System Software Version History. This article contains major errors:
In the first table, "System 2.0 Finder 1.1g" is a simple typographical error. It should be System 1.1 Finder 1.1g.
The first numbered "Macintosh System Software" release was version 5.0 in October 1987. The article assigns version numbers to earlier releases and presents a timeline. But the numbers are ill-conceived and the early timeline is simply not accurate. These mistakes then carry over to Apple's tech specs and other documentation for early Macintosh hardware online. See my discussion of how this mess was made: The develop CD and its spawn.
Understandably, this article has been widely used as a source of (mis)information on the Internet, including Wikipedia. Beware!
* "P" after the model number indicates a 220-240V power supply (Europe, Asia, Australia), as opposed to a 110-120V power supply (North America, Japan).
** M5011 was used for Macintosh SE machines configured with internal hard drives. This would later include the SE FDHD (SuperDrive), which replaced the SE in August 1989.
† Apple's recommended System file is version 2.0, with 3.2 as the maximum.
‡ Apple's recommended System file is version 3.2 (or 3.3 as an AppleShare client), with 4.1 as the maximum.
§ While both Macintosh SE and Macintosh II were introduced in March 1987, the II did not actually ship until April 1987, with System file version 4.1. See MacTech.
* The earliest references to "Macintosh System Software" are in the Read Me documents on the System 4.0 Finder 5.4 and System 4.1 Finder 5.5 disks. † System 3.3 (for the Macintosh 512K) was distributed on the Work Station Installer disk for versions 1.0 (with Finder 5.4) and 1.1 (with Finder 5.5) of the AppleShare file server.
‡ System 3.4 (for the Macintosh 512Ke) was distributed with AppleShare version 2.0 (with Finder 6.1).
The two training disks that came with the January 1984 software bundle used an early version of the Finder. The Macintosh icon is especially interesting, as it appears to show a prototype with a 5.25" disk drive like the first Lisa:
The System file used on the January 1984 System Disk and Write/Paint disks is, technically, "Version .97 14-Jan-84." This information was hidden from the user, for internal reference only. For the user, this was System 1.0 Finder 1.0. Font Mover was included on the Write/Paint disk.
System 1.1 supported at least two additional Finders, 2.6 and 3.4, both of which were distributed to developers for testing in early 1985, as documented in the MacTech archives—see the April and May letters to the editor.
System 2.0 Finder 4.1 was released in April 1985. [disk images] MacWrite 4.5 and MacPaint 1.5 were released, along with an update disk that featured the application System Update (a.k.a. Finder Update, its icon appears at the bottom of this page) that could be used to update any startup disk. The Update disk also included the Font/DA Mover application, a Fonts suitcase with one font in it [Taliesin, a pictorial font], and a "What's New" document. A complete System Disk was not released until June 1985.
System 2.1 Finder 5.0 was released on the first HD 20 Startup disk (with Hard Disk 20 1.0 and HD 20 Test 1.0) that shipped with the Hard Disk 20. Introduced support for the Hierarchical File System (HFS), although Apple did not announce it.
System 3.0 Finder 5.1 was released on the first Macintosh Plus System Tools disk. This same disk also came with the first 512Ke machines and the first Macintosh Plus Disk Drive Kit.
System 3.1 Finder 5.2 was only released on a Printer Installation (v1.0) [690-5075-A] disk that featured LaserWriter 3.0 and LaserWriter Namer 2.0. Apple intended to package System 3.1 Finder 5.2 with the first Macintosh 512Ke machines, but due to a bug they used the original Macintosh Plus System Tools disk instead. As a result, System 3.1 Finder 5.2 was never released as a system disk.
System 3.2 Finder 5.3 was released in June 1986. [disk images] In addition to separate 800K System Tools disks for the Macintosh Plus and 512Ke, along with a 400K HD 20 Startup disk (with Hard Disk 20 1.1 and HD 20 Test 1.1), Apple distributed two 400K update disks:
The System Installation (v1.0) disk came with two Installer scripts: "Mac Plus Update" and "External Drive."
The Printer Installation (v1.1) [690-5075-B] disk featured LaserWriter 3.1 and LaserWriter Namer 2.1.
System 4.0 Finder 5.4 was released in January 1987. It came on two 800K disks:
Macintosh System Tools (v1.0)
Macintosh Utilities (v1.0)
System 4.1 Finder 5.5 was released in April 1987. [disk images] It came on two 800K disks:
Macintosh System Tools (v2.0). Revised June 1987 (v2.0.1).
Macintosh Utilities (v2.0). Revised June 1987 (v2.0.1). Revised August 1987 (v2.1, two disks).
Macintosh System Software 5.0 and 5.1 came on four 800K disks: System Tools 1, System Tools 2 (Printers), Utilities 1, Utilities 2.
Macintosh System Software 6.06.0.5 came on four 800K disks: System Tools, Printing Tools, Utilities 1, Utilities 2.
Macintosh System Software 22.214.171.124.8 came on two 1.4 Mb (high-density) disks: System Startup and System Additions.
800K disks were also available.
Throughout 1987, Apple considered System file 3.2 (or 3.3 as an AppleShare client) to be the maximum for machines with 512K memory. By early 1988, however, this recommendation had been changed to System file 4.1:
From "A History of Macintosh System Software," Appendix A in Macintosh System Software User's Guide Version 6.0 (1988).
Macintosh 128K and 512K hardware
The following information reflects the current state of my knowledge of Macintosh 128K [M0001 and M0001P] and 512K [M0001W and M0001WP] hardware. It may not be complete, but it is accurate, based on personal experience and detailed reports from others, along with conclusions gleaned from the M0001 Registry.
There were three types of cases:
Early M0001 cases that read "Macintosh" on the back.
Later M0001 cases that read "Macintosh 128K" on the back. These are somewhat rare.
M0001W cases that read "Macintosh 512K" on the back.
Later Sony models OA-D34V-02 or OA-D34V-22. These models had a new insert/eject mechanism.
There were two series of external disk drives (model M0130):
Serial number started with D, made in USA.* The earliest of these contained Sony OA-D34V drives. Later they contained OA-D34V-02/22 drives.
Serial number started with Y, made in Japan.* These contained Sony OA-D34V-02/22 drives.
* There is a difference between the two in the coloration of the plastic case. The plastic used for the D drives is the same as that used for early Macintosh machines. The plastic used for the Y drives is slightly different and does not yellow, at least not nearly as much.
The first Macintosh 128K machines came with a plastic Macintosh box that included:
690-5003A "System Disk" disk: System 1.0 Finder 1.0
690-5002A "A Guided Tour of Macintosh" training disk
[A Guided Tour of Macintosh] audio tape
MacWrite and MacPaint came in a separate box that included:
690-5009A "MacWrite MacPaint" disk : MacWrite 1.0, MacPaint 1.0
690-5006A "MacWrite MacPaint: A Guided Tour" training disk
[A Guided Tour of MacWrite MacPaint] audio tape
In May 1984, the software bundle was updated and reorganized for System 1.1 Finder 1.1g. Font Mover and the additional fonts were moved to the System Disk in order to create more space on the MacWrite MacPaint disk and a new MacPaint disk was added. The two audio tapes remained the same, and MacWrite MacPaint still came in a separate box:
690-5003B "System Disk" disk: System 1.1 Finder 1.1g*
690-5002B "A Guided Tour of Macintosh" training disk
[A Guided Tour of Macintosh] audio tape
690-5009B "MacWrite MacPaint" disk : MacWrite 2.2, MacPaint 1.3
690-5011B "MacPaint" disk
690-5006B "MacWrite MacPaint: A Guided Tour" training disk
[A Guided Tour of MacWrite MacPaint] audio tape
In September 1984, with the introduction of the Macintosh 512K, the bundle was changed so that all the components would fit inside the plastic Macintosh box:
690-5003-C or 690-5003-D "System Disk" disk: System 1.1 Finder 1.1g*
690-5002-C "A Guided Tour of Macintosh" training disk
690-5006-C "MacWrite MacPaint: A Guided Tour" training disk
685-0011-A [A Guided Tour of Macintosh and MacWrite MacPaint] audio tape
Macintosh Plus and 512Ke hardware
All original Macintosh Plus [M0001A and M0001AP] machines had the words "Macintosh Plus" on the front and came with the M0110A extended keyboard. There were three generations:
"Beige" Macintosh Plus machines read "Macintosh Plus 1 Mb" on the back, with no copyright date. Beige was also the color of the Macintosh 128K and 512K, as well as the 512Ke.
In 1987, Apple changed the label on the back to read "Macintosh Plus 1 Mb" with a 1987 copyright date. The case color was changed to "platinum" to match the color of the new Macintosh II and SE machines. The owner's guide was redesigned and revised (see below).
In 1988, Apple changed the label on the back to read "Macintosh Plus" with a 1988 copyright date. The owner's guide was redesigned and revised again (see below).
There were two generations of Macintosh 512Ke [M0001E] machines:
Beige machines produced in 1986 have a label on the back with no copyright date. They came with the M0110 standard keyboard and contained first-revision Macintosh Plus ROMs.
The location and design of the Apple logo on the front of the machine was the same as the original Macintosh and the 512K.
Platinum machines have a 1987 copyright date on the label. They came with the M0110A extended keyboard and contained second-revision Macintosh Plus ROMs.
The location and design of the Apple logo on the front of the machine was the same as the Plus. At the time, Apple considered System 3.2 Finder 5.3 to be the maximum for machines with 512K of memory. [It was only later that System 4.1 Finder 5.4 was declared the maximum.] This fact probably explains why no effort was made to update the 512Ke owner's guide and software bundle in 1987, while the Plus received a complete overhaul.
Note: I have never seen a M0001E with a 220-240V power supply.
The Macintosh 512K/800 [M0001D] was a 512Ke with a M0110A extended keyboard. Like the first-generation 512Ke, the location and design of the Apple logo on the front of the machine was the same as the original Macintosh and the 512K.
I don't know if the 512K/800 existed as a platinum machine. It is possible that it was only sold within the education market with "Macintosh ED" printed on the front.
Note: I have never seen a M0001D with a 110-120V power supply.
The Macintosh ED [M0001ED] was a 512K/800 [M0001D] packaged for sale to educational institutions. There appear to be four editions of these machines:
Beige with M0001ED model number. [Serial numbers begin with F, for Fremont, California]
Platinum with M0001ED model number. [F]
Beige with "Macintosh ED" printed on the front and M0001D model number on the back. [Serial numbers begin with C, for Cork, Ireland.]
Platinum with "Macintosh ED" printed on the front and M0001D model number on the back. [C]
Note: I have never seen a M0001ED with a 110-120V power supply.
Macintosh Plus ED
The Macintosh Plus ED was a platinum Macintosh Plus with "Macintosh Plus ED" printed on the front and a standard 220-240V M0001AP model number on the back.
Macintosh Plus and 512Ke manuals
Changes in the design of the Macintosh Plus owner's guide (and packaging) parallel the changes in the hardware.
In October 1987, the software bundle was updated for Macintosh System Software 5.0, on four disks: System Tools 1, System Tools 2 (Printers), Utilities 1, Utilities 2.
In April 1988, the software bundle was updated for Macintosh System Software 6.0, on four disks: System Tools, Printing Tools, Utilities 1, Utilities 2. The training disk was updated and HyperCard was added to the box:
690-5209-A "Your Apple Tour of the Macintosh Plus" training disk (v2.0)
"HyperCard and Stacks"
The Macintosh 512Ke was introduced in March 1986. It came with the Macintosh Plus System Tools disk:
690-5064-A "Macintosh Plus: System Tools" disk (v1.0, System 3.0 Finder 5.1) 
690-5090-A "Macintosh 512K enhanced: A Guided Tour" training disk
[Macintosh 512K enhanced: A Guided Tour] audio tape
In June 1986, the System Tools disk was updated for System 3.2 Finder 5.3 and the Macintosh 512Ke:
690-5091-A "Macintosh 512K enhanced: System Tools" disk (v1.0) 
Sales of the Macintosh 512Ke continued until September 1987, but evidently the software bundle did not change after June 1986. For more on this, see above.
Macintosh 128K/512K required Macintosh Plus Disk Drive Kit (above).
Replaced 128K/512K/512Ke logic board with Plus logic board.
Replaced 128K/512K/512Ke back panel with Plus back panel. Machines upgraded with this kit thus read "Macintosh Plus 1 Mb" on the back, but don't say "Macintosh Plus" on the front.
Included current Macintosh Plus owner's guide.
Macintosh Plus memory upgrades. Result was a Macintosh Plus with up to 4 Mb of memory.
Replaced 256K plug-in memory modules with 1 Mb modules. You could replace either two or four modules, resulting in 2560K (2.5 Mb) or 4096K (4 Mb) of memory.
* As far as I know, this is the only printed Apple manual that tells you how to initialize single-sided 400K disks in the HFS format. Requires Finder 5.x or 6.x: "Holding down the Option key while you click One-Sided (or if the disk is in a 400K disk drive, holding the Option key down while you press the Return key after you've named it) installs the hierarchical file system on just one side of the disk. Use disks initialized this way with updated startup disks only." In other words, they can't be used as startup disks. Or else!