I was bored, so I reverse-engineered the AR marker encoding. I made an Excel spreadsheet that generates the AR marker for any Pokémon (including ones not in the Pokédex app yet).
XLSX download
XLS download
I made it using Excel 2008 for Mac, but it should work with any version of Excel. Just select a Pokémon from the drop-down menu (or type its name in the box), and it will display the marker.
Pokémon before Victini and after Kyurem won't work (they're not programmed in to the Pokédex), but I'm fairly certain their codes will work once they're added. Also, I haven't checked the order of the alternate forms, so they might be a bit off.
If you want to know how it works, the marker encodes a 10-bit number (0 - 1023). The lower 9 bits are encoded around the outside, using white as a 1 and black as a 0 - starting from the lower left and going anticlockwise, the bit order is 036147258 (i.e. corners first, then anticlockwise from the corner pixel). The last 3 pixels of the outside are checksums (for each group of 3 bits in the 9 encoded bits). The inner 4 pixels take 1 of 2 possible configurations depending on the 10th bit of the number (bit 9); the middle lower left is always white, and the middle upper right is always black. I assume the lower right encodes the bit, and the upper left is a checksum, but I'm not certain (there is no need to encode an 11th or 12th bit, as there are only 728 Pokémon/forms).
The base form of each species is encoded by its national dex number - 1 (from 0: Bulbasaur to 648: Genesect). Alternate forms follow (from 649: Unown B to 724: some form of Genesect), and finally, the 5th gen gender 'alternate forms' (725: Unfezant, 726: Frillish, 727: Jellicent). The numbering works out exactly.
As a final note, has anyone noticed that the backgrounds of the stickers all depict the same AR code (rather than that of the Pokémon on the sticker)? Try drawing/printing the code and scanning it in!
If you can't be bothered, it's