Go here:
http://www.frontiernet.net/~Spyle/FFXI/ffxi.html
This is the one I have been using and it works well. You don't have to be running in windowed mode, but it helps.
All the program does is "parse", or separate, the information in the log files, adding up damage and curing statistics and organizing it into a easy to read summary.
Keep in mind that the stats are not 100% correct as the parser cannot calculate DoT spells. It can only parse statistics that appear in your log window, and are not filtered out.