A lot of classics have been mentioned already, but here's some MST3K lines from my own experience.
From the Movie:
* "Let's see. . . Shatner, Shatner, Shatner--nope. He's not in this one. We're safe."
* "G.I. Joe action set--Nerdy Joe not included."
* "Da da da da da da! It's the Brak show, starring me I'm Brak! It's the Brak show, & I've got lots of good guests! Da da da dut da da da . . ."
* "Whoa, the Howells' hut is really nice!"
* "They're hickory curing them."
* "Place your hands over the bars. Now they're magnetized."--"And if your hands were made out of metal, that would mean something."
* "Mike broke the Hubble! Mike broke the Hubble!"
* "Whoa! I didn't expect this!"
* "Oh, well, look at that, 'Breach Hull--All Die!' Even had it underlined!"
From TV episodes:
* "Trumpy, NO!"
* "Watch out for snakes!"
* "Mitchell!"
* "Whoa, Torgo's been hittin' the ThighMaster."
And, of course, there are new, a few recent quotes from that net phenomenon known as Strongbad:
* "Trogdor!"
* (person making techno music sounds) "The system is down!"
That's jut a few (that I can remember currently).