I never knew how time-consuming this would be! I figured I'd share what I've done (am doing).
I personally have been using a big pair of cutting pliers (hopefully those are the best words to describe it). Just something to break out the plastic notches. I've done about 15 cases thus far, and I've already got a nice blister on one of my fingers to show for it (from the handles of the pliers).
After that, to get rid of the jagged edges left behind from the pliers, I then use a dremel tool to shave it down, so it's more flush for the game to sit in the case properly. This can also get a bit messy/sloppy, with bits of semi-melted plastic shavings flying around - both onto the surround floors, and even all over myself, my hair, face (wear safety googles!) and clothes. To be honest, after I'm done with the dremel, I usually spray myself (along with the cases) with an air compressor that's in my workshop. Seems to be the best method of getting rid of all the random plastic shavings that fly off each UGC case when you're modifying them.
Anyways, just wanted to share my experiences. I've got about 50,60 NES games to do, so it's going to take a while to get them all done and properly in cases! Time consuming, but after seeing them on the shelf, it really looks sharp, and that the hard work is indeed worthwhile.