Tables that aren't UPDATED often and aren't huge tend to be faster with myisam. innodb has row-level locks, whilst myisam only has table-level locks. None of the tables in eqemu are really huge, so it's the locking that's going to make the biggest difference on tables that have frequent updates. Innodb also clusters data about the primary key, so SELECTs are quicker when the WHERE clause uses that key.
So I would hesitate to convert everything to innodb unless you have extremely fast drives, although any table that might have concurrent writes to different rows could be quicker with innodb.
I've noticed a marked slowdown on build 488 vs the 450's, with higher loads on mysql. I suspect there was a query introduced that would benefit from better indexing.
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