When I rack my brains for terrible endings, Philips CD-i comes into mind...
In Hotel Mario, when you complete the game, you see Mario and Luigi getting kissed by Princess Peach, and then you are given the title of "Best Player Ever".
...as well as some of the games that AVGN played to the end (or otherwise cheated to the end).
I think that Ghostbusters game does it worst. It's just several lines of text that's worded wrongly. "Go and rest our heroes!"? WHAT IN THE NINE HELLS OF...
Death Rally also comes into mind. The game was great for its time, and I especially like the introduction, but the ending is just a bit abrupt.
You shoot up the main bad guy, The Adversary, you see his car burn, and then this guy says that The Adversary is dying in his burning car and that his reign is over. LIKE DUH, if I killed him, I can see him die on the cutscene; I don't need some deep booming voice to tell me what I'm seeing!
Good endings? Hmm...
Duke Nukem 3D does it pretty well, I think.
At the end of Episode 1, he shoots the boss in the head and says, "I'm Duke Nukem, and I'm coming to get the rest of you alien bastards!"
At the end of Episode 2, he holds true his promise to the boss before the final fight, which is to "rip off your face and $#!^ down your neck!".
At the end of Episode 3, he kicks out the eye of the boss through a goal-post and says, "Game over!".
At the end of Episode 4, he sticks a pipebomb into the womb of the Alien Queen, says, "It's time to abort your whole freaking species!" and blows her to bits ... underwater.
Bejeweled 2 Deluxe
Puzzle Mode's ending is a bit odd, but the music and backdrops are pretty nice, and that weird jewel-composed face is pretty interesting. You don't get to see that anywhere else in the game.