I would have to say that the most over-CRed monster in 3.5 is the Devastation Beetle. Spot and Listen +6, no special detection besides darkvision, can't fly or teleport, has no attacks at greater range than 60 ft., has no means of affecting incorporeal creatures. CR 50.
I mean yes, it has nearly 3000 HP, its lowest save is +42, it's got SR 60 and DR 20/-, its land speed is 70 ft., and it does 30d10+24 trample + a 6d6/round acid aura, but it literally loses to Walls of Force + (Shadow or Cloudkill or Melf's Acid Arrow), and that's just in core. It doesn't even have the Tarrasque's set of immunities, regeneration, or DR/epic to potentially (yes, I know, the RAW's weird) let it hit incorporeal.
The other really obvious case of an over-CRed monster is the Shrieker, which is CR 1 despite being unable to move or attack in any way.
@awaken_D_M_golem: Kobold wizard 17 isn't CR 14. The CR = level - 3 text only applies to kobolds with NPC classes, which Wizard is not. Also, the Races of the Dragon web enhancement (though not RotD itself) is explicitly intended to improve kobolds to parity, so it'd be more than a little mean as DM to use that material and then still count kobolds as weak.