I'll second "Sacred Ground"; I've always thought that that episode gave us a really nice look into Janeway's spirituality and her own internal conflict between her spiritual beliefs and her scientific beliefs.
Though "Threshold" is bad, I do agree that it is funny, in an insane, ridiculous way. The scene with Tuvok and Chakotay on the planet is downright hilarious!
I'll probably get some guff for this one, but I feel like "The Fight" is one to mention. Don't get me wrong, it's not a stellar episode, but it gives us a brief glimpse into Chakotay's character beyond the plank on the bridge (for once).
Oh, and someone mentioned the TNG episode "Genesis" a little ways back. Great episode in terms of the creepy factor, but definitely not one to be watched at two in the morning...