Talahassee is probably one of the best albums start to finish. The Sunset Tree is also a stand out. I love pretty much anything Darnielle touches though
Both of those albums refer heavily to "the alpha couple" which is basically his theme for a couple whose co-dependence through addiction (and overall bad decisions) has transformed their love into something very deep and twisted. So when you hear him say "I hope you die, I hope we both die" it at first sounds childish and funny, but when put into context has a very deep meaning.
Probably my favorite song that really breathes this theme is this one:
http://www.youtube.com/watch?v=hSLDkIJnNF8&feature=related
He also does a lot of lo-fi recordings, so if you can get past the low sound quality he has put out a lot of great material.
Not sure if it's been mentioned, or if he's considered indie or not, but I also really dig (dug?) Elliott Smith.
I notoriously dislike optimistic music....I'm not sure why. I guess it just feels disingenuous to me.