Anything and everything bearing the Etrian Odyssey name. No debate on that one. All of them range from $10-20, and they are loaded with incredible depth and substance!
And when will we see EO 5 in America?? C'mon Atlus USA get on it!
Other games I would pay more than they sell for include:
DS Chrono Trigger
Final Fantasy Tactics Advance series (GBA and DS)
Capcom's Onimusha series
and almost every retro download that sells for cheap today.
What are yours?
Unfortunately, I'd have to go way way back, to find something I thought was a great deal. It's not because I don't believe there are (or have been) good deals out there but rather because I almost never buy or play new games any more.
I would say Outlaw Volleyball was the most underpriced game with a high production and replay value in years. The gameplay was spectacular, and it was only like a $9.99 game IIRC. Before that, I'd say The Guardian Legend, for the NES. People either love it or hate it, but it came out at only $20 locally. It's one of my favorite games, blending shooter an RPG elements, with pretty spectacular graphics for the bosses at the time.