I know that the Poke talk has died down, but here is my list:
Boss Signatures:
Gym Leaders: Onix, Starmie, Raichu, Venomoth (Appears in both Koga's Yellow and Janine's rosters), Alakazam, Rapidash, Rhydon
Elite 4: Lapras, Machamp, Gengar, Dragonite
Gary *swearword* Oak!: Exeggutor, Arcanine, Gyarados
Gen 1 near-mandatories that aren't covered by the above: Snorlax, Aerodactyl
(the other 2 fossils are path-split but Aero can be obtained easily enough; Lapras would also have been included were it not Lorelei's Signature Pokemon. Snorlax is also on Red's team in GSC and HG/SS) With Lapras replacing Espeon in the latter
Given that 3 of the 4 "Trade-Onlys" are part of the GL/Elite list, I'll go ahead and add Golem. But not as a replacement for Onix. Onix is in because of Brock.
You will notice that there is no Grass-type Pokemon among the GLs. That is because while Brock still has Onix even in his Heart Gold/Soul Silver After-Game Rematch and Giovanni doesn't use Rhydon, Erika's Tangela evolves into a Tangrowth for the HG/SS AG Rematch, and so would be lumped in with Gen 4 Pokemon. (I had heard a rumor that Garchomp was banned from Official Tournaments, but its Bulbapedia entry did not refer to such a ban. If such a ban is in place, I would put it at the head of the Gen 4 list)
Next up: What about Final Fantasy 4: The After Years? I know it's a Wii game but between being a continuation and being on WiiWare instead of a disc, I'd say it's the Wii game most likely to be added. It's a better pick than DPPt, which will probably be shoveled off with Felix, Jenna, Sheba, and Piers.
The likelyhood of ranking for FF4:TAY will influence whether I buy it next week (to finish in time for ranking) or just wait for my B-Day in February (where I'll definitely finish it before the next ranking in June).