Have to agree with Umbra upon this.
I used a tweak tool back in the days, but they stopped coding it, it had tons of pages with options for everything related to the OS, probably the best tweaking tool that was ever made, never saw anything that got even close.
Tried some other tools after that but most always ended up with giving trouble or not doing anything at all.
So I started to tweak everything manually and made scripts for everything that worked out for me, updating them for every service pack and Windows edition change.
I use those scripts upon a clean install, quick and easy and I always know what they do.
I might code a C# version of it one day where everything is selectable and explained, since I don't really want to hand out them scripts, there is to much that needs to be explained since some settings will break functions that some people use.
One size doesn't fit all, a lot of people writing tweaking guides forget just that, same goes for many tweaking tool developers.
For cleaning CCleaner + CCEnhancer covers almost everything, the few additional files and registry entires that I clean are done manually, but in most cases it's best just to leave those files and entries alone since deleting them might cause issues.
Regardless of what people choose, always do a system backup first.