Most underrated? Hm.
Moyashimon comes to mind. It was really good, though odd. It had some really interesting characters. It was about a guy who could see microbes and his life at an agricultural college. It was also pretty progressive and had a (serious) crossdressing character.
Genshiken is an anime about college otaku. Actually, it's also very progressive and has a (serious) crossdresser. The first "anime" in the video isn't real, it's an anime they watch inside the anime.
Abenobashi Mahou Shotengai was amazing. It was about two kids who get kicked from world to world, each one getting crazier than the last. It's also really deep, as well, as the whole thing is basically a metaphor for running away from reality. It features a crossdresser (not serious). It's utterly ridiculous and has a ton of references.
As always, it's a crime how few people have seen Yozakura Quartet: Hana no Uta. It's unique and amazing and has awesome characters, both good and evil.
Finally, Skip Beat. It's one of my favorite anime and I can't believe how little it gets mentioned. It's so good at bouncing back and forth between emotions and the story itself is really interesting. Some of the best scenes gave me goosebumps.
