Here's what I do.
First, I use J River Media center for managing everything. It's not free, but it's pretty cheap.
Next, I make SURE every single MP3 is properly tagged, including album art. I also make sure the art is embedded in the MP3. It chews up a little more space, but it means that I can use just about any decent library program to repull all the info direct from the MP3's in the event of a catastrophe.
next, I use FILLCD to gather up as many full albums as will fit on a single DVD. So what I end up with is a folder structure like this.
MP3
DVD1
Artist
Album
Actual tracks
DVD2
etc.
That way, it's trivial to backup portions of my collection to DVD's and restore them if there's a prob. I also back up to USB HD, but I like belt and suspenders for this particular data.
Then, all I have to do is point at the root MP3 folder and scan all subdirs. Media center can do that easily. But most any other decent Library manager should be able to do that. Even Windows Media Center can.
If everything's tagged, the tags are read in, and databased so that searches are instant once the initial scan is complete.
And if you get a virus or something corrupts a bunch of your files, you can just grab the DVD, copy it back over and rescan.
It's a little work, but not bad with the right tools.
Last note, Personally, I wouldn't bother with any app that makes you put your tracks in a specific folder structure or be named in a specific format. All that info should be in the tags. If things are tagged, all those tag values should be databased for instant retrieval. The folder structure shouldn't matter at all. But that's me. Some people really do care how the folders are laid out. In fact, a decent library app should be able to rename the files and also relocate your MP3s into a folder structure based on the tag values in the tracks themselves. MC can definitely do that, but I know others can too.