TehFix, I have a similar problem with self-esteem. I think I'm ok - I just sometimes have trouble believing that others could possibly share that opinion. But I'm working on it, and have found that with practice it can get easier to 'be yourself' around others and to worry less about being judged. (Lots of practice. Just chill. etc. etc.)
As for problems with one's self ...
I used to have no problem whatsoever with my ass, although I knew it was bigger than it should be if you go by media values. Then a while ago I had something of an epiphany, and suddenly thought that it was too big. This fortunately didn't last for very long, althogh it did re-occur at least once for a short time. Then I decided that it was functional, gave me something to sit on, made my legs work, and if you really want to go into the asthetics side of things (a minor issue, since I can't see it anyway without a craned neck or two mirrors) ... some blokes actually like larger behinds. About the only real problem with it is when clothes fit strangely, due to being standardised shapes.
Continuing with the Lament of the Pear Shape, I also have had varying opinions of my bust. It's exceptionally small, to the point of being hard to find bras for (that's an entirely seperate issue) ... but, this has the plus side of a) being less stared at by random men and b) making jumping and hopping (things that I tend to do) far more comfortable.
On the issue of bras, though - why do designers of these garments assume that if you're small-chested, you must want to be bigger? So many of the things are padded, underwired or both, that finding one that is neither is a pretty rare achievement.
Oh, and my hands are quite small. It would make playing the piano quite difficult.
I also can only run for pathetically short distances before losing my breath and getting a pain in both my head and my chest, due to being asthmatic.
And my toenails are very unhealthy, too thick, and sometimes grow at slightly odd angles. I'm going to have to get them checked soon to see if there's something medically wrong with them.
Something else that could be said to be unconventional is my opinion of my weight - again, I see my body size and shape as functional, a case of fair enough if you like it and fair enough if you don't; I don't mind it, and I think that that's ulimately what counts the most. I'm not exactly overweight, could stand to be more toned but so far haven't put the time into getting myself that way ... and ultimately, I have a fairly average figure that is comfortably between 'too fat to function' and 'so thin you can see my bones'.
Phew, long post.