Are there any good mangas where an attractive female falls for a not-so-attractive male? There are so many shoujos out there where a "plain" girl and a "super hot" guy fall in love, but is there any that are the other way around?

Angel Densetsu - He's scary-looking rather than plain-looking though.

Nana to Kaoru
Accel World (though I've been following the anime version on hulu rather than the manga)

Shoujos, right?
Bara wo Karasu Te de Boku wo Dake
Hibi Chouchou maybe?
Saruyama!

I would definitely have to second Nana to Kaoru, it's really good - really good from a romance perspective.

Not sure I would put Hibi Chouchou in that category, they are both relatively attractive.

Both Angel Densetsu and Ocha Nigosu (to some degree) fall into this category but the romances are both ridiculously slow - the romance barely exists for 98% of the story IMO.

Also, there are quite a few that have 'plain' male, but not necessarily unattractive. Are you looking for something like that also or do you want the butt-ugly male protagonist?

Hmm, good point. I guess I didn't word myself very carefully. In the sense of shoujo, I rather like it when the male is considered "plain" or even "unattractive." It doesn't really matter to me. He could be just an ordinary, everyday, average Joe or he could be considered someone unattractive. I'm kind of tired of reading shoujos where the girl is considered "plain" or "unattractive" (in most cases, she isn't, she's actually quite pretty) and the guy is super handsome. It annoys me to no end. Especially since the girls usually have an inferiority complex, and it continually pops up in the plot.

On another hand, thanks for your reply and your opinions!

In that case try:

Love Hina - one of my firsts and favorites
Change 123
Good Ending - to a lesser degree
I's
Monkey High - don't get thrown off by the name, it's good and no one acts stupidly (which is rare in romances)

B Gata H Kei fits this EXACTLY... it's a good manga too!

Utopia (NEUK Dae Sam) seems to be heading in that direction (judging by the summary), but it actually hasn't gotten to the romance part yet (well... not in the translated chapters, at least). The guy went through some sort of accident that scarred his face and he has a prosthetic leg.

Other than that...as far as your normal, average joe male characters they are below...
my heart is beating
nineteen, twenty one
bonnouji
bitou lollipop

I think that troupe shows up a lot in shounen/stuff targeted towards guys...(it seems like if it's targeted towards girls, it's plain girl/handsome guys, if it's target towards guys its beautiful girl/plain guy, which I don't think is what your looking for, since it has a lot of the same problems as the typical shoujo stories but also sometimes really objectifies women)

There's a few shoujo stories that break the mold though (I think they're usually better for it!)

Dengeki Love Machine
The first story in this collection fits exactly the trope you are looking for. And it's by Tomoko Hayakawa, the mangaka of Perfectt Girl Evolution/the Wallflower so the quality is pretty high.

Hanada
I don't really remember much about this one other than it fits the trope you're looking for and was cute.

Cyboy
This is basically the exact opposite of the typical shoujo dynamic. Plain guy tries to become super handsome, has complex about looks. Super adorable!

Warau Kanoko-sama and it's sequel [urlhttp://www.mangaupdates.com/series.html?id=48874=]Koi dana ai dano[/url]
On the surface it's about a handsome guy and plain (for real, plain) girl, but I think this fits what you're looking for, because it's actually the girl that is awesome one! Of the two, she is totally the one with the power!

Ciel
For the first few chapters, the main beautiful character totally falls for a plain(ish) guy. Not really a romance though, and if you only want that romance then you prob won't like this (although it is a super awesome read! But it's more of a fantasy than romance)

Aitsu no Daihonmei
This is exactly what you are looking for! Except it is shounen ai... It's funny and cute and I totally recommend it if you don't mind shounen ai.

I think a lot of Kamio Youko's stories (Matsuri Special, Hana Yori Dango) kind of fit as well, since she seems to really like making the heroine start out liking the cool looking dude, and then switch to falling in love with the dorky looking one.