Calling Zoot a PIM is like calling me Lance Armstrong. The learning curve is steep (I'm still discovering things I can do with it after 8 years, and I'm not a power user), but the pay-off is tremendous. One flaw is it doesn't handle formatted text.
Swish-e is a fast, flexible, and free open source system for indexing collections of Web pages or other files. Swish-e is ideally suited for collections of a million documents or smaller.