Pixelmon has a handy page that details the available Pixelmon, as well as a page that overviews their overall progress.
In total there are currently 197 distinct species in Pixelmon. One thing that may be a bit of a hurdle for this, depending on if you are playing by yourself, or on a server with other people: several of these Pixelmon require trading (with or without holding a specific item) to reach their final evolution.
Going through the pages (as of Pixelmon version 4.1.3):
Generation 1: 100% complete. 78 distinctive species. Some notes:
- Mewtwo is obtained by using Mew with a cloning machine
- Eevee, the Hitmon ('-Chan', '-Lee', and gen2's '-Top'), Slowpoke and Poliwag all have branching evolution paths. You'd need to breed 6 additional Eevee, 2 additional Tyrogue, an additional Slowpoke, and an additional Poliwag.
- Porygon does not spawn normally in the wild, it has a 1% chance to spawn next to the player when they craft a PC
Generation 2: 100% complete. 52 distinctive species. Some notes:
- Many of the Pixelmon are not counted because they are either pre-evolutions or all new evolutions to previously counted Pixelmon.
- Unown is a bit of a problem, at it has 28 forms. If you must have one of each, add 27 to the count, as I only counted it once.
Generation 3: 63/135 - 46.667% complete. 32 distinctive species. Some notes:
- You'll need to breed an additional Ralts for the branching evolution
Generation 4: 43/107 - 40.187% complete. 12 distinctive species. Some notes:
- About a third of the completed Pixelmon for this generation currently are new (pre-)evolutions to previous species.
Generation 5: 53/156 - 33.974% complete. 23 distinctive species. (no notes here)
This gets a little complicated, depending on your filing system. The PC limits you to 16 boxes of 30 by default and there are 17 types. This can be expanded up to 256 boxes of 30 by editing the config files, so you are fairly well covered if you need to be.
If you look into the Wiki's page for each individual type (example: Normal) to see what you are in for, you might initially break that down into to evolution families and find that there are 32. But this is deceiving, as a number of those 32 are birds that are Normal/Flying, and a few are like Eevee or Swablu, whose evolutions lack the Normal typing.
If you have a single box for each type, you might run into problems in certain areas, particularly as the devs continue to develop the mod and slowly add in more and more Pixelmon. I counted the Bulbapedia page for the Water type, and there are around 30 Pokémon whose evolution chains end in a pure water type. That doesn't even count Water/X or X/Water. Many of these are not in the mod yet, but it creates the question; Do you file a Water/Rock Pixelmon (Corsola) under Water, or Rock? What about a Rock/Water (several of the fossils) Pixelmon?
If you use a seperate box for each combination of types (probably wise to ignore the order of those types in this case; Water/Rock would be filed into the same box as Rock/Water)... you would have quite a few boxes with few Pixelmon in them, but you would also be somewhat future-proof as Pixelmon gets updated.
The alternative is to start making judgement calls as a box fills up, shunting things into the comparatively empty boxes of their second type. Normal, Flying, Fire, and Water would seem to be boxes that would fill up the most, requiring judgement calls on which ones get filed under their secondary types.