Rebuilding an InnoDB table index is easy in MySQL 5.0. Simply type:

mysql> ALTER TABLE table_name ENGINE=InnoDB;

Warning: When dealing with large databases, this can place a lot of load on your DB.

In MySQL 5.0 it is possible to drop unqiue constraints but, the syntax is not incredibly intuitive.

alter table TABLE_NAME drop index UNIQUE_CONSTRAINT_NAME;

Code Ghar provides a more thorough description.