Well, I can tell you that the reason they get left behind is because they were created AFTER the program was installed, so the uninstaller has no idea they exist.
That being said, the Windows registry is probably something best left forgotten by anyone who isn't a professional programmer or tester/debugger. That includes registry cleaners/fixers/whatever which have a long sorted history with causing people to wind up with a bricked system. As far as I'm concerned, the whole lot of them are nothing more than a scam. Absolutely none of them will offer up any kind of information on the selection criteria used, which screams snake oil to me.
There are a bunch of myths floating about regarding the registry. How it's some secret repository of hidden tweaks, or that removing unneeded entries will speed up your system. As with pretty much every myth, they aren't true. You go spelunking in the registry at your own peril, and will tend to get little sympathy from anyone here if you break something. And if you're looking to reclaims space, the registry is the last place you should be looking. The most you'll likely ever save from the registry is a few bytes.
There are books on the registry from Microsoft's publication arm Microsoft Press, but they're all written for programmers by programmers. Mostly because those are the only people who should be messing around in there. If you've reached a level where you can understand that book, odds are you can use the information in it wisely, or at least safely.
I don't bother with utility programs. I think it's important you know how to do the tasks yourself first. Like learning the multiplication table. Once you can do things for yourself if need be, you can make the choice to use some program, and be in a position to assess them all on your own.
Now, if you're looking to gain a lot of firsthand experience with malware detection and removal, keep right on using IE. Otherwise, I'd strongly suggest any other browser. I'll leave it to others to debate why, I'm content with the fact that IE is the ONLY browser that has any kind of malware problem... Period. It has tens of thousands, if not millions, of unique bits of malware... All other browsers might have a dozen or less. I don't care how bad at math you might be, those are easy odds to calculate. Can't do much about buying an Acer system now, but maybe you'll be one of the lucky few who gets a working system.
I know when you delete any installed software it will not totally delete ,, For instance I recently installed and deleted I-Tunes. I have an application that can analyze the registry and found that I-Tunes left a list 5 miles long.. (google earth) which I installed and deleted 3 times left a giant swath on my hard drive also. Some others don't leave as much.
I am an interested amatuer and know enough about the registry and this utility software I have, to do an educated crash on my laptop. 3 times already. My repair guy looks at me funny.
So, how can I get some space back in my hard drive, probably a couple of Gigs.. Are there any really good utilty programs I shoud know about? I would really like to know this registry stuff. Can you recommend a book !!
I am doing all of this in an Acer Aspire 1640 notebook SP3 and IE8 updated. It is about 4 years old but it works great !!