Hmm its a lazy saturday morning and I just discovered this thread. Just thought I'd point out that I wrote the libprs500 GUI to solve exactly these problems for myself. At the moment it supports metadata extraction from LRF and RTF files, will add PDF later. Also its designed around the concept that a single logical book can be implemented in various formats. It has backend support for the SONY reader and soon for the REB 1100 thanks to ashkulz. Also it will have the ability to convert various formats to LRF. It has the ability to display ebook lists sorted by various criteria as well as searching metadata.
Ofcourse it still in its early stages so not everything works as well as it should, but its open source and cross platform, so its only going to get better with time ;-)