At the time, I obviously thought this was the 500th comic, but as you can see from the comic counter, this is actually the 501st. And if you count the special comic, this is actually the 502nd.
For most of the comic, I never bothered keeping count. Some comics, such as MS Paint Masterpieces and pretty much all the hosted comics, keep count by just numbering the comics as they're made. I preferred to keep track by date, where each comic had a date code based on "YYMMDD". So, for example, this comic went up on August 28th, 2001, so its filename is "010828.png".
When I last upgraded the archival code, I decided to throw in a comic counter, just to see how many comics I'd actually made, so I had to write a little algorithm that just counts how many days it's been since the comic started. This works because there's a comic for every day except for two breaks in September 2000 and December 2001, which are just removed from the count.
And in case you're wondering, the total count comes to 2658, not counting the special comic.