You shouldn't have any problem - MySQL's query support doesn't change, just the internals. One downside to InnoDB is that it takes up quite a bit more disk space, but the advantage of row-level locking (as opposed to locking the entire table) can be quite significant, especially for busy databases.
Jason Rhinelander
Gossamer Threads
jason@gossamer-threads.com
Jason Rhinelander
Gossamer Threads
jason@gossamer-threads.com