Well, after trying to figure it out for several weeks now (no, it hasn't been the only thing I've been doing), I think I may have nailed how Hasbro came to their magic "500" number with very little fudging on their part, but a lot on mine. Here's a little backstory:
When the 300th Fett came out in 2001, the back of the package had a list of the 300 figures to that point. The list included the figures from the Droids and Ewoks lines and its pre-300 ended with Plo Koon from the POTJ wave just before the Fett was released. It was with that in mind that I started to modify 301-500, but I had to do something interesting to get it down that far.
First of all, I pissed all over Hasbro's list and removed the Droids and Ewoks figures. I've never considered them a part of the basic action figures line, due to the stylistic differences, so they both went out the window, as did the Animated Clone Wars figures. Given Hasbro's selective attention, I figured they wouldn't be above forgetting the Ewoks and Droids lines when coming up with 500 either.
Now, on the 300th Fett packaging, Luke was 1, Carbonite Han was 100, Mara Jade was 200, and Fett was 300. Since Hasbro counted Luke as 1, I went with that, but the ditching of the Ewoks and Droids figures brought Han out of 100, leaving it wide open for... the POTF2 version of Darth Vader.
Basically, figures 1 through 96 is the vintage line (with C-3P0 with Removable Limbs and R2-D2 with Periscope and R2-D2 with Lightsaber all included). 97 begins the POTF2 line with, again, Luke Skywalker, and after that it's in alphabetical order by wave. Darth Vader is the third non-Luke figure in POTF2 alphabetically, so he's number 100.
Now, funnily enough, using this logic, figure number 200 is no longer Mara Jade, but...the POTF2 Flashback Anakin Skywalker. Even in alphabetical order, it still wound up that way without any of my tinkering.
Which brings us to figure 300, which I kept as Boba Fett, but in doing so, I had to move the formerly 299 Plo Koon back a bit, and 299 is now the end of the Fan's Choice Ellors Madak wave, and that figure is Sabe. Boba Fett still comes in a "break" in the sequence of basic action figures, but he comes a bit later in the game.
Strangely enough, we keep the Skywalker tradition going with figure number 400 who is, again, I'm not fudging things, Padme Amidala (Lars Homestead) from the 2004 Saga lineup. At that point, things were just too eerie for me, but I pressed on nonetheless.
And figure 500 is, of course, Darth Vader, but who was just before and who was just after him? Figure 499 is the ROTS Destroyer Droid (figure number 44) and Figure 501 is the ROTS Tarkin (figure number 45).
Now, as for what was and wasn't included:
Now Included: R2-D2 with Sensorscope, R2-D2 with Lightsaber, C-3P0 with Removable Limbs (Vintage)
Not Included: Variations of the Battle Droid (Episode I), Scout Trooper (POTJ), Battle Droid (Saga 2002), Rebel Fleet Trooper (Saga 2002), Imperial Officer (Saga 2002), any recard of a figure without major changes for any reason (e.g. 31 of the OTC line), the Droids and Ewok vintage lines, and the Animated Clone Wars lines.
Is it accurate? Probably not, but it's the closest I could come after about 25 different tries to get things to match up. If there is interest (and the mods don't mind the massive list), I'd be more than happy to post it here.