I don't think emptying the prefetch folder is a very good idea. Yes it does lessen the boot time (by a few meagre seconds) but it also lengthens application load times by more than a few meagre seconds when you add them all up, :lol:. A good idea to decrease boot times is to use MS Bootvis to optimize boot files.
http://www.majorgeeks.com/download.php?det=664
Also use of a good registry cleaner, I use Regcleaner (
http://www.worldstart.com/weekly-dow...cleaner4.3.htm ), it's free and fast. It also works well in conjunction with CCleaner.
Using a launcher application like Colibri or Launchy (can be found in the downloads section, here) also helps you to save time.