For those unfamiliar with the concept here is a lazy link to Episode Six, and with that @SabreMau's fabulous presentation and links to the previous threads/utilities:
forums.penny-arcade.com/discussion/143512/tome-of-comic-edits-return-of-the-continuing-saga/p1
Everyone has a different way of doing this. Sometimes you see a PA comic, the expressions on the faces, and you think "Whoa, this TOTALLY should be about Wile E Coyote and the Road Runner instead of some videogame". First, check if you've been abusing funny substances and if not, go ahead and think up a new dialogue.
Sometimes, If you feel the URGE to edit a comic but you have no ideas, it helps when you just blank out all the balloons and look at the drawings. Maybe change the order of the panels. Weird ideas might come to you.
Often, the way someone/something is drawn might remind you of some popular person/thing/topic and well, you're off aren't you. Sometimes another thread or forum just hands it to you on a platter.
Read the official PA archive if you haven't done it yet. You're going to need the panels one day...
edit: alternative PA search engine provided by Rehab:
I relied upon Pipe Four to find for me. If you don't use it you really should as its much better than the Archive search engine here!