Muad'Dib

The main problem is that neither science nor mathematics can answer the question of whether the hidden "messages" in the Hebrew text of the Torah are intentional. At best it can calculate the probability of such messages occurring by chance (and every calculation I've seen toward this end has yielded disgracefully high odds).

As such, even if there are a few scientists ("top" or otherwise) who buy into the Bible Codes, they are not accepting them in their capacty as scientists. Now if the probability is in their opinion low enough that they feel compelled to accept that the messages were planted there by a divine force, that is a conclusion that they have arrived at in a (by definition) non-scientific manner; but I've never seen calculations that have even tempted me to take the claims of the Bible Code folks seriously.

Big Spoon

I've seen it demonstrated on TV many times that the codes could esily have arisen by chance - they do in any novel you could care to mention.
Using statistical concepts understandable by the layperson (but not gullible christians, apparently) it can be thoroughly debunked.

Quetzal

Here are a couple of articles from Skeptical Inquirer magazine by David Thomas. Hidden Messages and The Bible Code and another follow up article a year later. The latter article is the one where Thomas talks about deriving an assassination prediction from Moby Dick. If you have access to the SI hard copy edition, Thomas has yet another article in the Mar-Apr 03 issue.