Contrary to popular belief, Prefetch is there for a reason. The entre idea of prefetch is to pre-load components for programs that you use often to speed up their launch. Prefetch does not contain any "vital" components for running programs, but is actually just an optimization that microsoft built into the operating system. Deleting the prefetch data has a SLIGHTLY positive effect on boot time, but slows down the launch of your commonly used programs. Deleting all prefetch data does more harm than good, although microsoft does say that it can sometimes have a slightly detrimental effect on EWF performance, but this is not a consideration for almost any PC users. The space that you (temporarily) save is insignificant, but the decrease in performance is noticeable.
I just ran some program opening benchmarks on my laptop, which measured the opening (time from execution start to window appearing) speed for three of my programs (twice per program), deleted all prefetch data, rebooted, and ran again. The Result was an average of a 19.627% drop in program opening speed.
Although I admit I did not do this in a perfectly controlled environment (such as a fresh virtual machine), this is a significant enough change for me to say that deleting all prefetch data is a mistake.
If you still believe that prefetch is a waste of space, you can disable it by following Microsoft's instructions here.