Strangely enough, many of my favorite movies have been MST3Ked. And they were favorites before I knew of MST3K...
Hangar 18 - Gary Collins is an astronaut who is blamed for the death of a colleague when he is accident killed when a satellite they were launching strikes a UFO.
Also stars Darren McGavin as a NASA scientist, Stuart Pankin as a drunk, and Robert Vaughn as the villainous something or other, who orders the coverup of the UFO that crashed into the satellite.
It's a fascinating movie because you have the chase of Gary Collins across the country looking for clues to the UFO, being harassed by MIB, and at the same time, Darren McGavin's team of scientists unlock the mystery of the aliens...
The Crawling Eye - Forrest Tucker (the guy from F Troop) is a UN Investigator called in by a friend to investigate a problem in Trollenberg, a tiny town in the alps. It seems that local climbers are being beheaded mysteriously.
The story gets a bit convoluted, with two sisters who do a mind reading act (one of whom is both absolutely beautiful and a psychic) and reanimated dead people. But it's really something that could have been written by HP Lovecraft, only hurt by bad special effects.
Earth vs The Spider - Set in the 50s, a girl's father mysteriously vanishing while buying her a birthday present. She and her dopey boyfriend go looking for it, and come across a giant spider, which through the machinations of the local high school science teacher, runs amok in the town.
Not MST3Ked (but probably could be):
The Blob (both versions) - Original has Steve McQueen and a great depiction of teenage life in the 50s, 80s has Kevin Dillon and ditto for the 80s. Great special effects, too, by any standard. Also Shawnee Smith and the delectable Candy Clark.
The Thing (both versions) - Original isn't like the story much, but is probably the best B monster movie ever made. Snappy dialogue, good acting by a cast that can't act (as shown in all the other movies they did).
John Carpenter's version is a lot like the story, but updated to the 70s/80s and grimmer. Probably the best horror movie every made.
Amityville 3-D - Greatest haunted house movie ever. Sampled extensively by My Life With the Thrill Kill Kult. Also stars Candy Clark and middle aged Meg Ryan playing a teen ager.
The Resurrected - An adaption of HPL's The Case of Charles Dexter Ward. Very much a B movie, but really well done, including realistic gore (very gorey)