You can try Kazoku Game - eccentric/quirky male lead. 
winnie - Added!  Thank you. :)
good doctor ............. niceand simple main lead is as u like
i remember you ........ a genious main lead ...... ending is not so great
amitspiky - Added!  Thank you. :)
Cheese in Trap has an eccentric male lead. He is not quirky or fun but he is strange... Secret Garden also has an eccentric male lead :)
Love Me If You Dare. Bo Jin Yan is one eccentric male lead I love :)
I'd recommend from your PTW list:
City Hall
Death Note
I Remember You
Jenius

Not on your list : Heart to Heart (kdrama) and Monster (jdrama)
Some other japanese ones : 
Kagi no kakatta heya
Legal High
Date
Mahoro Ekimae Bangaichi
maybe Densha Otoko, Dokushin Kizoku and Nazotoki wa... not sure they are eccentric enough
Mikushi, Nadia, wsa67, SumiTheCat - Thanks very much! :)

I'm not sure if I should add these two or not: Death Note and Heart to Heart. 

I haven't seen the new Death Note remake yet.  Is "L" as prominent in this one as he was in the anime and live-action movies?

And it's been a while since I've watched Heart to Heart, but I only remember the female lead being really strange.  Or was the male lead a bit eccentric as well?

SumiTheCat - Since you're not sure about Densha Otoko, Dokushin Kizoku, and Nazotoki wa Dinner no Ato de, I'll leave them off the list for now.  If anyone else thinks any of those should be on the list, please let me know!  (I've only seen the movie version of Densha Otoko, and remember him being very shy rather than "eccentric".  Or is he different in the drama version?)
In Heart to Heart the male lead is a little eccentric, but not as much as she is.
I liked the Death Note drama, but " L"  is different from both the anime and moviesI didn't care for him as much in the drama.
Here's my contribution: 
Keizoku Spec 2 (Jdrama) - the male and female lead are both an oddball. The lead guy is a police officer who has a penchant on tracking bad guys and he uses a brown paper bag as his everyday bag. If that's not weird enough... I'd recommend "The Master's Sun" Kdrama instead.

Hyde, Jeckyll, Me (Kdrama) - another drama where the guy pretty much has a dual personality which makes him eccentric at some point. 
@Neyjour : 
I think you're right regarding my last 3 rec : Densha Otoka male lead is an otaku, pretty shy as you said, but not really an eccentric. yet his way of life makes him look like an outcast.
regarding Dokushin Kizoku, the male lead is a bachelor proud of his condition and telling what he really thinks to other people. that lead him being avoided. he has some habits, but that doesn't really make him an eccentric in the way you may want.
as for Nazotoki, the male lead is not really an eccentric, though he says what ever he wants to the woman he is working for.
When thinking more about it, those dramas are probably not what you want. I do recommend the three of them though, they are quite good. for Densha otoko, i'd rather the drama over the movie.
By the way, thanks for the thread, i would take a closer look at that list you're making, i like eccentric leads as well!
Maybe Falling for innocence?? I mean he's not a genius but his behavior is always bizarre (in the best way possible :P)