General Discussion

Name some of the hidden gems you've found on your quest for quality anime and manga. For me, It's gotta be Desert Punk and Rainbow. Desert punk is just really fun. It's got enough humor and action to keep you entertained throughout the series. From what I can tell, not too many people know about this anime, which also has a manga that followed a different fork in the road, but I can't seem to find it. Second is Rainbow which is a lot more recent (april of last year). It's not really your standard anime. It's about 6 new prisoners (although they're in a "school"), young men, who've been taken in a few years after the atom bomb attacks. In the prison they gain a leader that they call their brother who becomes a mentor to them. Together they go through many trials and tribulations while having to deal with the wicked and brutal senior guard, Ishihara, as well as Sasaki, the perverted doctor of the school/prison. Eventually they attempt to escape and live out their dreams, but I won't spoil what happens next.  

I enjoyed Desert Punk the anime, but felt it needed a second season to fully explain the turn of events in the latter few episodes. 

It was impossible to find translated copies of the mange for a long time, but you can find the first 5 or so of the 14 volumes already released in Japan in English now.  The manga is different than the anime in several respects too from its look to its sense of humor.  I don't read too much manga but this one has interested me since I saw the anime years ago because of how unsatisfying I found the conclusion.   
 
Tenshi na Konamaiki (aka Cheeky Angel) is probably my current favorite hidden gem and it joined my Top-10 list recently.  Still, I know full well it won't appeal to most other anime fans since the animation is sub par by modern design standards (it looks a lot like the manga) and the story is a bit cliché; however I became involved in the premise and the interplay between the characters.  It's a reverse harem comedy about a girl who was magically transformed from a boy several years ago and is still adjusting to the gender switch.  Back when she was a boy, she found a genie of sorts and wished to be the the manliest of men; however genies being genies, she was turned into the loveliest of women.   What's different is that unlike Ranma from Ranma1/2, she doesn't completely reject her feminine side.  Perhaps this is because, unlike Ranma, she is stuck with her new gender all the time.  Still, she wants to return to her original state and so she searches for the genie again to turn her back into a boy.  The series opens with her first day in high school.  Being an especially attractive young woman, she quickly acquires herself a "fan club" that eventually includes the school's toughest delinquent and a would-be samurai.  I really enjoyed watching her struggle with love and attraction during the course of the show's 50 episode run.  Incidentally, all 20 volumes of the manga are available in English for reading, if interested.  But, the anime ended with me feeling warm and (mostly) satisfied.  That's one of the things I value in a show.

I found the Kannagi manga to be quite enjoyable. 
there's also Fujimura-kun mates, which is also quite good.

@H2Oyea: I agree about Rainbow, it was really quite good! 
 
I'd say my favourite under the radar is probably either Beck : Mongolian Chop Squad or Welcome to the NHK.  For manga, i'd probably say it's Jojo's Bizarre Adventure, even though it has pretty strong sales it seems like it's often overlooked.

I have no idea what would be a hidden gem since I don't talk to to many people (who watch anime... this should have been there in the original post :p) but I don't personally know anyone who has watched Minami-ke. I found that series very relaxing and fun. It's a slice of life type show with no plot that focuses around the three Minami sisters.

I'm the only person who knows what Suicide Island is.

Maoh Juvenile Remix as well as Switch, Dolls, and No. 6