Try SEO Powersuit or IBP.They both helpfull.

Ran into the same problem myself to be honest, few months back, there are plently of different ways you can handle it, depending on how you work and a load of other factors, for example if you swap between systems quite a lot, if you work on both your laptop and desktop, then you'lll want to look into syncing, then you've got the question of, do i just use a ftp server? or shall i get dropbox? or maybe I should use google docs, well if I'm going to use google docs, then should I get google apps as well?

But more to the point, whatever you decide to go with, make a folder for each project, try to keep them looking the same, for example in each folder, have a backlinking report file, a keyword research file, a sub-folder for content/articles, another sub-folder for MYSQL backups etc.