There was long played scalability issue with InnoDB auto-increment field. For details check Bug 16979. In short words the problem is in case of insert into table with auto-increment column the special AUTO_INC table level lock is obtained, instead of usual row-level locks. With many concurrent inserted threads this causes serious scalability problems, and in our consulting practice we had a lot of customers who was affected by InnoDB auto-inc. For several of them we even advised to replace auto-inc column by that or another solution.
Good news is the bug is fixed. Bad news is it is fixed only 5.1.22, which is not released yet.
I wonder if the fix is going to be ported to 5.0, as I mentioned it affected many production systems and not all of them are ready to upgrade to 5.1.
The interesting also is the fix introduces new system variable innodb_autoinc_lock_mode which determines behavior of InnoDB for tables with autoinc. I do not want to copy-paste MySQL documentation, the very good and informative description of the problem and solution is available here.