Have you tried Delicious Library?
There used to be an app named Libra at http://www.getlibra.com but it looks like it is no longer functional. I had loaded quite a few book of my own into it.
A Windows clone (or close cousin) of Delicious Library is MediaMan
An open-source alternative might be Calibre, but I haven't tried it. Looks very interesting, though.
The one thing I've found is these solutions don't do full-text searching of your eBooks. For that, you will need something that can search PDFs, CHMs, etc. Google Desktop Search would be the answer to that.
For my own software library I tend to use Launchy's indexing service. It's a pretty light weight application launcher, and it does not require you to type in the exact name of a file. This is pretty handy on my PC where I have about 10GB of eBooks (I doubt I'll ever read even 5% of it). Whenever I want to read up on a certain topic I just start typing in key words and a list of matches appears in front of me :D
Have you tried out Calibre. It's open source, but starting to look more professional than it did a while ago.