It seems that there is at least 7 universes in this "cluster":
Earth-21913 (Next-Gen version)
Spider-Man (Xbox)
Spider-Man 2 (PS2/Xbox/GameCube)
Spider-Man 3 (PS3/Xbox 360)
Earth-???? (GBA version)
Spider-Man (GBA)
Spider-Man 2 (GBA)
Spider-Man 3 (GBA)
Earth-???? (DS version)
Spider-Man (GBA) (?)
Spider-Man 2 (DS)
Spider-Man 3 (DS)
Earth-???? (Old-Gen version)
Spider-Man (Xbox)
Spider-Man 2 (PSP)
Spider-Man 3 (PSP/PS2/Wii)
Earth-???? (PC version)
Spider-Man (Xbox)
Spider-Man 2 (Windows/Mac)
Spider-Man 3 (Windows)
Earth-???? (N-Gage version)
Spider-Man 2 (N-Gage)
Earth-???? (Mobile Phone version)
Spider-Man 3 (Mobile Phone)
Notes
-The GBA version of Spider-Man 1 also in the DS universe is more of a headcanon, since they are all Nintendo handleds, you know.
-Calypso didn't appear in the PC version of Spider-Man 2, so I don't know if that is accounted for in the PC version of 3. If not, then PC 3 would probably be an alternative sequel of PS2/Xbox/GameCube 2.
-The Xbox version must be the canon version of the first game console version since all PC, Next-Gen and Old-Gen versions of 3 have Spider-Man having met Kraven the Hunter before.
-At the end of GBA 1 Mary Jane says "Goblin and his cronies are in jail", implying that he actually survived the final battle (luckily it seems that GBA 3 Harry doesn't even mention that he died, so maybe he only wants revenge towards Spider-Man for putting his father in jail?). In GBA 2 Mary Jane wonders if Doc Ock survived the explosion, and while Spider-Man thinks he didn't, the ending slide shows he is wrong. The ending slide of GBA 3 shows that the symbionte escaped and is implied that Eddie survived too. So maybe the Friend or Foe universes are close to the GBA universe, since all of the villains survive there? (But not the same one, since Mysterio is in GBA 2, but Peter doesn't know him in FoF)