If you want foreign keys, you have to go with InnoDB. I'll never go back to non-Innodb for that reason.
Just be aware you can't use any cute tricks any more like copying all the files (tables and indexes) with the same name to another location as a backup. ALL DATA is physically located in one file - so for multiple databases belonging to different accounts, there's no longer the transparent method of reading the size of that folder (their database) or allowing them to backup the contents of that folder. You have to really depend on mySQL at that point. If I could have both worlds I'd take it but relational tables are a must for me.
sam