If we go by M$ definition of "Clean Boot", read here:
http://support.microsoft.com/kb/310353Windows optimization apply to number of actions. It all depends on personal needs.
Among others, it'd be: uninstalling unnecessary programs, play with startups, virtual memory, etc., but also doing some cleaning procedures: cleaning temp files, running defrag.
In general, bringing Windows to a state where there is nothing unneeded running, or staying on your hard drive.