dtgreene: If you're talking about overpowered setups in D&D, keep in mind that 3.5e admits the monstrosity that is Pun-Pun.
[url=http://www.dandwiki.com/wiki/Pun-Pun_(3.5e_Optimized_Character_Build]http://www.dandwiki.com/wiki/Pun-Pun_(3.5e_Optimized_Character_Build)[/url])
(What happens here is that the build uses polymorph and an ability to get the target form's supernatural abilities to get an ability that was never intended to be player usable, and in gaining the ability, manages to break the entire game.)
ValamirCleaver: That cheese build relies upon a lot of incorrect rules-lawyering. It falsely assumes one can use all the magical abilities of the assumed form while polymorphed. It is erroneously listed as a 3.5e Optimized Character Build. It relies upon a 3.0 feat, Assume Supernatural Ability, that was not reintroduced in a 3.5 publication. Therefore the build cannot be replicated as either a pure 3.0 build nor a pure 3.5 build. It also mixes material from the Forgotten Realms and Eberron settings. Not that any of this would matter to detractors of 3rd Edition or 3.5...
Actually, the original version of the build did not require anything from 3.0. The essential ingredients were as follows:
Egoist (from Expanded Psionics Handbook (XPH)): Allows access to the Metamorphosis power (from XPH), which works like the "Polymorph Self" spell, complete with all the issues involved.
Metamorphic Transfer feat (from XPH): This allows the use of a supernatural ability from the assumed form. This is how the Manipulate Form ability is aquired. (Note that, unlike Assume Supernatural Ability, this ability was printed in a 3.5 publication.) Supposedly, this can only be used 3 times a day, but the description doesn't clarify what that means for passive abilities. (Manipulate Form is active, so it is clear how the limit applies, except for using it to give your psicrystal (or kobold henchman) Manipulate form.)
Psicrystal Affinity feat (again, from XPH): This gives you a psicrystal that you use Metamorphosis on to turn into a scaled one, to act as a target for your first Manipulate Form.
(Overchannel from XPH is used in the build, but it's technically optional; it just makes the build possible at level 12 rather than level 14.)
In other words, the build is possible in 3.5 alone.
I consider the existence of this build to be evidence of one specific issue: Polymorph effects are too broad because the list of creatures you can change into is open-ended. (Then again, the wiki article mentions a few other ways to get that ability.)
If, as a DM, you do not want to allow this build, the best way to deal with it is to put some sane limits on polymorph effects. Simply restricting the forms to those in the Monster Manual is a good start; that way adding a new monster to the game doesn't risk giving the player access to an ability that PCs were not intended to have.
Edit: Actually, if you don't like psionics and are willing to wait until level 17, you can use the Shapechange spell (from the Player's Handbook) to change into a form and get the supernatural abilities of that form. In other words, the only thing outside of the core rulebooks that this exploit requires is the Surrukh monster entry so you can get Manipulate Form; your actual build doesn't actually need anything outside the core rulebooks. (Of note: I believe you need 3.5 Shapechange, as I don't think 3.0 Shapechange gives supernatural abilities.)