I agree, but I think an argument can be made for “Pumped Up Kick” sounding melodically upbeat. As much as I dislike the song, it sounds breezy and fun to me, and if you look around the net, that’s not an uncommon perception of the song. Heck, even the Wikipedia article has this to say: “The song was written and recorded by frontman Mark Foster while he was working as a commercial jingle writer. Contrasting with the upbeat musical composition, the lyrics describe the homicidal thoughts of a troubled youth.”
Not to menton Maxwell’s Silver Hammer, which is a lot more out front with the darkness in the lyrics but still has a bouncy, whimsical kind of sound to it.
Warren Zevon’s Excitable Boy.
The music is very upbeat, but the lyrics are all about rape, murder and insanity.
For extra bonus marks, I even heard it played at a high school dance! 
Tom Waits’ “Frank’s Wild Years”.Not really upbeat but kinda smoooth.
I am disappoint no one mentioned Violent Femmes http://www.youtube.com/watch?v=DZNBZj2BKvU
I love the bouncy, cheerful tune of the Smiths’ “Girlfriend in a Coma.”
The Sign by Ace Of Base is a song about being over someone, wondering how they could have loved the person, how you have to make yourself feel happy, etc. It’s a fairly sad song in content but it is SO happy and just always makes you FEEL so happy 
But it works because it’s about feeling better about realizing the truth about a crappy relationship and being over it, so not really too much of a contradiction.
Mack The Knife is a great contribution to the thread earlier and I wanted to 2nd it. One of my favorite songs but with the lyrics “lies a body just oozing life” you know you’re listening to something pretty dark.
Butcher Pete is a song about a rapist “he’s hackin and wackin and smackin!” It’s the most fun you’ll ever have singing about rape, it really is the original hide your kids, hide your wives, hide your husbands too because he’s raping everybody up in here, song And part 2 also celebrates raped people waiting in line to be raped some more! Yay!!!
Most of the works of the Cherry Poppin’ Daddies fit this thread very well. Their big hit, “Zoot Suit Riot” is about actual riots that occurred in Los Angeles in the 1940s but it sounds like an upbeat dance tune of the era. “Drunk Daddy” is about a child abuse victim but its so upbeat and danceable too!
Bad Moon Rising by Creedence Clearwater Revival.
Possum Kingdom by The Toadies is kinda catchy.
Folsom Prison Blues by Johnny Cash
I used To Love Her by Guns And Roses
Lovefool by The Cardigans is very depressing to me.
And, of course, that goes for the Beautiful South, too…
Well, that’s if you’re going on Bobby Darin’s version. If you listen to the version that comes straight from the Threepenny Opera (“Moritat”), it is much more dissonant and harsh-sounding, and the more direct translation of the lyrics (which were much more loosely translated for “Mack the Knife”) were much more graphic. (There’s a reference to an arson that killed seven children and an underage widow who got raped.)
You’ll hear both versions in the movie Quiz Show…the bouncy Darin version in the beginning and the harsher, spookier “Moritat” sung by Lyle Lovett at the end.
Yup, that’s exactly how I always heard it. I used to own the album (well, cassette tape) that song appeared on, and I think it included the lyrics in the liner notes. Can’t verify now, since I no longer have it.
‘Weird Al’ Yankovic is a master of the upbeat music/dark lyrics technique:
Steely Dan have made a career of songs like that.
“Veronica,” by Elvis Costello.
Joshua James: The New Love Song.
Another “upbeat” but bleak Springsteen song is widely regarded as a Dave Edmunds osng: “From Small THings (Big Things One Day Come).”
The music is very cheery, but it’s about a woman who abandons her husband and kids to go on the road with some jerk that she eventually kills. She spends most of her life in prison, while her kids grow up without her.
Pink Floyd’s “Free Four” is a very upbeat sounding tune about getting old and dying. I tried to find a YouTube link, but they are all “blocked in my country.”
What I came in to say.
*You are my sunshine, my only sunshine
You make me happy when skies are gray
You’ll never know dear, how much I love you
Please don’t take my sunshine away
You told me once dear, you really loved me
And no one else could come between
But now you’ve left me and you love another
And you have shattered all my dreams*
Oh! Listen To The Mockingbird is a classic one of these! It’s so bouncy and whimsical it was actually one of the Three Stooges’ themes, but it’s about the singer’s dead lover.