The "great" thing about sad songs is how some thing can strike us and not others depending on what we've lived through...
My votes and reasonings:
Something Corporate: I woke up in a Car. About the time the song got popular I was on really rocky times with the first real long term relationship I'd ever had. She went away on internship in Poughkeepsie and never came back to me. It was kinda a growing apart that neither of us wanted be neither of us could stop, exactly what the songs about.
As mentioned earlier, Season of Love from the rent soundtrack, while not nessisarily sad, causes a lot of emotion in me... it really strikes at bring back a flood of memories, both really great and really sad.
Evaporated by Ben Folds Five is great at achieving what it wants to as well.
Dashboard Confessional: Standard Lines. Anyone who has ever, ever ended a relationship that they didn't want to because it had to be done can't help but cringe at this song. Sometimes, things are just better that way even though we know that they aren't going to be really.
Jared Campbell: Fate. Great example of an upbeat song that can rip through you.