Here are some of the ones I found that seem out of place. Keep in mind I find it easier to find undervalued players than overvalued ones, so there are a lot more of those. Of course, these are just my own opinions:
Too High (push them down):
Gagne at 3.
Loaiza at 33. If he repeats, I'll eat my hat.
Hoffman at 56 is too high. Very risky to take him that soon.
Griffey at 100 is too high, in a 12 team league, this is the 7th round. Way too early with his recent history.
Batista at 150 is ranked ahead of Vidro, Isringhausen, JuanGon, and others. Unless the league ignores strikeouts and batting avg, he's too high here.
Posednik at 110. I would never take him this high until he proves he can do it more than once.
Too Low (move them up):
Vlad at 40 (obviously)
Rivera at 44
Prior at 17
Becket at 137 is too low, worth a top 100 pick, IMO.
Matt Morris at 114 seems pretty low.
Jeter at 115.
Mike Sweeney at 164 is pretty low, I think.
Blalock at 173 seems low.
Cliff Floyd at 200.
H Matsui at 202.
Hampton at 209
Hinkse at 233.
Teixeira at 258 (especially in a keeper league, this is low)
Rhodes at 280 is low, assuming he keeps the closer job.
Phelps at 283 is low. When Delgado gets traded, he will be the starting 1B in Toronto.
Aurilia at 313
Konerko at 317
Drew at 325
Nick Johnson at 337
Robbie Alomar at 347. I don't think he's completely done yet.
Kearns at 349.
Reyes at 429 (especially in a keeper)
Burnett at 476.
There's probably more, but these are ones I saw with a quick look through.