- Goldeneye on the N64 — James Bond franchise rights issues. There was a "reimagining" developed and release, but it's an entirely different game.
- Panzer Dragoon Saga on the Sega Saturn — IIRC the source code was lost, and a combination of that, Saturn emulation being tricky, the relatively small number of highly in-demand exclusive releases for the Saturn, and Sega no longer releasing their own consoles mean that official emulated Saturn support for the title is unlikely.
[EDIT] I should add that the situation of these two games in particular is made worse by the less-than-stellar state of open source emulation for those systems, especially in the case of the Saturn. I think it's fair to say that both are in a worse state than the Playstation, or even the newer Gamecube/Wii thanks to Dolphin.