The Voyager crash sequence was amazin'.
Captain La Forge and the Starship Challenger!
Lone survivors Chakotay & Harry.
Just all around awesomness.
I did read somewhere that early on, Chakotay's love interest was supposed to have been his daughter, instead. Wish they had kept that, since it would have been a bigger sacrifice on his part to alter the timeline.
Timeless is my favourite too
Year of Hell is probably very close behind, although I'm not sure if that is cheating, since it's a 2 parter.
Timeless has always stuck with me, because it has one of those teasers designed specifically to be as great a teaser as possible and gets you excited for the episode. And it's a great story, with one of VOY's best CG sequences of Voyager crashing, accompanied by a musical score that really elevates it into a classic scene.