Correct me if I'm wrong but I believe it is still the 'suggested' MySQL for the emulator... I know many people still use at least 4.0.23 so even if it's not supported on the MySQL sites, it is still supported in this community in so far as the compatibility of the emulator...
That being said, moving to the newer stuff is 'typically' better and I believe someone (cavedude no?) had posted some potential bench mark related stuff with the engines suggesting 5+ is better for larger servers and 4.1 was better for small servers making me wonder what 4.0.23 would be good for... but to each their own.
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