It's not as terrible as it first seems, if you stop the MySQL daemon and then go into your data directory, you can directly rename the files that represent the tables.
For instance, say your database files are in /databases, your database name is "foo" and your table name is "bar", but your PHP code refers to a table named "BAR" in "FOO".
If you look in /databases you'll find a directory called "foo", you'll need to mv this to "FOO". once you've done that, look inside it to see the files representing the tables. For every table there are three files: .frm .MYI .MYD
In our example, you would rename bar.frm to BAR.frm, bar.MYI to BAR.MYI, and bar.MYD to BAR.MYD (note that the extension is case sensitive and should never change.)
If you have a ton of these things to change, I would recommend writing a shell script to do it. Alternatively, if you like the mousey approach, just pick up a copy of MySQLFront from www.mysqlfront.de It's an excellent GUI interface for the MySQL Database that supports renaming tables (can't rename databases though). Hope this helps some. 🙂
-Sheff