Anime where the protagonist has no skills or talents, whatsoever?

Katekyo Hitman Reborn (Tsuna)

Elfin Lied (Kouta)

Sekirei (Minato)

Rosario+Vampire (Tsukune)

Inuyasha (Kagome, Shippo)

Neon Genesis Evangelion (Shinji)

Bleach (Orihime, Rukia)

Naruto (Sakura)

Tsubasa Chronicles (Sakura)

Clannad (Sonohara)

I've heard that Tantei Opera Milky Holmes is built around basically this premise; the main characters originally had super powers, but got them confiscated and are hilariously useless without them.

Out of what I've actually seen? Hmm. Haibane Renmei sort of has this, in that the main character can't figure out what she's good at or what she's supposed to do with her life (she is eventually given a job, but it's to atone for a mistake she made, rather than because she's particularly good at it). In Angel Beats, the MC is actually a certified doctor, but never has any need to operate in that capacity during the show, and doesn't seem to have any other particular skills. And the male lead of Angel Tales seems to have no particular talents, although he does eventually succeed in school and become a veterinarian.

haha... you saw Greg's question.

I don't know. Every character has to have something their good at, or else you wont have any conflict or strife in the plot. The audience won't like a character that is "completely" useless.

If you are talking about characters that are weak, both in mind and body, then I have only one suggestion: that damned whiner, ungrateful brat Shinji Ikari from the anime, Evangelion. That kid is a complete coward, a cry baby. Pretty much a waste of pen and paper. I admit, I barely made it through around 7 episodes. But believe me, I tried to like that anime, but the "uselessness" of that griping brat ruined it for me.

Clannad

Lucky Star

there are alot of Anime out there with very Generic "Nothing Special" characters

I'd guess around 80% of all harem anime. For starters Keitaro from Love Hina