Spotlight: ACH Toolset
The ACH toolset is a web-based application to analyze how various evidence fits several competing hypotheses. It was originally developed for the intelligence community.
This is a great tool for investigators because it forces you to build different explanations and analyze how various pieces of evidence fit that explanation. This is a big improvement from the yep, that looks like a ghost approach.
To use the software you will need ACH a Linux server with Apache 2, PHP 5 and MySQL 5. I know that sounds complicated, but a quick trip to GoDaddy will get you setup for a few bucks a month.
Go to CompetingHypotheses.org to get the software or more info.