We use UeberP to manage consultancy projects for a department with great results in practice. The revision management system and no-nonsense interface are ideal for regular use, and the backend database design can handle masses of files. Brilliant!
Webazlier + Zeus Web Server
There is a patched version of Webalizer which processes Zeus Web Server binary logs - http://support.zeus.com/products/v3/webalizer.html. Since these logs are around 4x smaller than normal ones, they're handy when performance or storage are critical. Webalizer runs a little faster on these too.