Great Thread! Many tools listed in here I use frequently.
I'm glad to see Hijackthis on here it's tops in my book. You might add this site to the OP.
http://hijackthis.de/ I've used it quite frequently. Copy and paste your log (or upload the txt file) and the webpage gives you an online analysis. Some people are hesitant to post information from their computer on a forum and this would be an option for them.