Metroid II: DX (Gameboy Color) - Basically a colorized GBC port of the Gameboy original, but still, it saddens me that Nintendo opted to release it. At least some fans did an admirable effort to re-create it, but even so, nothing beats playing an actual cartridge (as opposed to emulating).
Starfox 2 for Super Nintendo - This game was friggin' finished when Nintendo pulled the plug on it, all because of company politics. Nintendo thought Starfox would be a more effective franchise on N64, and so they decided they wanted to increase fan pining by making them wait for Starfox 64. Many elements from Starfox 2 ended up in Starfox 64, but even so this was a very bone-headed decision on Ninty's part and a major disservice to fans (what's worse is that they don't even want to release it on Virtual Console).
Sonic Xtreme (Sega Saturn) - Some very passionate and talented young developers were working very hard on this game, and they made some excellent progress until corporate bickering at the top of Sega caused the project to collapse. It was pretty much a month away from being finished, and the project's leader literally almost killed himself to get the game finished. Sega put the Saturn's killer app in the hands of a little league team, and even though it looks like they might have actually succeeded, Sega still managed to kill what could have been one of the Saturn's most noteworthy titles.
Metroid Dread (Nintendo DS) - frankly, I think that the Metroid games that Nintendo has put on the DS so far are crap. Metroid Prime Pinball, despite having somewhat decent gameplay, was basically a joke. I mean, what's next, Metal Gear Poker? As for Prime Hunters, I thought the game was a disappointment for me too, since it was basically a bland Doom clone set in the Metroid universe. Metroid Dread would have been a TRUE Metroid game for the DS, made by the team behind Super Metroid, Metroid Fusion, and Metroid Zero Mission. A classic 2D style Metroid would have been a great antidote for the radical departure of Metroid Prime Hunters, so it's very disappointing that this project is going no-where. As of now, the Metroid franchise appears to be on hiatus, possibly due to the underperformance of Metroid Prime 3 (a game which I also have some major beefs with, but that's for another thread).
Shenmue 2 (Sega Dreamcast) - I'm one of those kooks who was obsessed with Shenmue when it came out. Looking back, the gameplay left a lot to be desired, but at the time it was the most immersive game I'd ever played, and largely still is. When the Dreamcast got canned, I threw a royal fit, but I at least could take comfort in the fact that Shenmue 2 would be the system's last hurrah-- until Micro$oft swooped in like a flock of vultures, and snatched the game out of our hands a month in order to woo the now homeless Sega fans to their neighborhood. To this day I think Sega was probably sabotaged by Microsoft spies, but that's a story for another day. The point is, I never got to play Shenmue 2 until I learned the wonders of torrents, and I will not soon forgive MS for their treachery against my Sega habit.
Half-Life (Dreamcast) - like Shenmue 2, this game was all set and ready to go, and would have been one of the last good games for the system. Even though I had the PC version, I was eagerly anticipating this version's enhanced graphics and new gameplay, plus being able to play it from the comfort of my couch. Unfortunately, when Valve began work on a PS2 version, Sony paid Sierra to cancel the Dreamcast version. Given that the Dreamcast was on its deathbed, it probably didn't take much to convince them not to release it on Dreamcast. Like Shenmue 2, you can get the finished game on a torrent, but again, it was a major burn.
Earthbound 64 / Mother 3 (Nintendo 64) - This game was also almost finished, but Nintendo pulled the plug on it since it utilized the abysmally unsuccessful 64DD, which never came to America. It's a shame they weren't willing to just rework some parts of the game to make it run on just a cart, the N64 was seriously hurting when it came to RPGs.