The method I use for splitting logs is that at the start of a night, I enable combat logging. Before every boss attempt, I use an Ornate Spyglass (
http://www.thottbot.com/i5507) to give myself the "Longsight" buff.
At the end of the night, I grab the logfile and split it based on the string "You gain Longsight" and then prune out any wipes from there. I then feed the individual kill logs to WWS and get a nice neat set of kill parses.
It's easy enough to split based on a standard string and anyone can use the spyglass (as opposed to class abilities like Sentry Totem).