It might be helpful to review exactly what the registry is and what it was meant to do. The Windows Registry
A lot of people will say Windows 7 registy is not the same as Windows 98 or even Windows XP. And that's certainly true. But the basic underlying function is still the same . . . It keeps track of all software installed on the computer and (perhaps most importantly) how each program relates to and interacts with all the other programs on the computer. And this is where many registry editors/cleaners give the appearance that they're not doing the cleanup very well.
Let's say you uninstall Program A. It's very possible that Program A hooked itself into a couple hundred registry keys, and some of those keys belong to Program B and Program C. A registry cleaner (at least the reputable ones) will err on the side of caution and NOT remove the registry entries JUST IN CASE they are still needed by Programs B and C. Personally, I'd rather have a few hundred or even a few thousand unneeded registry entries than to have a program crash because a needed key was mistakenly removed.
And to repeat an often stated fact, Windows 7 is not your father's Windows XP where tweaks and cleaners were the norm in order to keep XP working the way it was supposed to.