Accidentally Accurate: He comments on how we aren't given any context for why Subaru and Seishirou are fighting to the death in X, and speculates that one caught the other cheating on them with their immigrant landscaper Raoul. While the exact circumstances are off, he did get the Homoerotic Subtext (which only just avoids crossing into text in the actual series) exactly right.
The Engineer as well. His character has a pretty sizable hatred of Bennett and he goes to a number of lengths to insult, mock, and belittle him. The commentaries make it clear that they are friends and Marc even mentions that he's almost uncomfortable with how mean his character is, with Bennett laughing it up and loving all the grief the Engineer gives Sage.
Throw It In: According to his commentary, the part in Twilight of the Cockroaches where Bennett holds the video box upside down was actually a complete accident that he didn't notice until later.
What Could Have Been: When doing Nuts and Bolts, Bennett and Marc frequently discuss bits that they had to cut from their scripts.
In Ninja Resurrection they wanted Darcy Lord, the Australian Brodouche God, from Lady Death to make another appearance, but due to conflicts with the actor's scheduling they could not.
In the Fist of the North Star review Ben and Gabe (with a cameo from David, the title card artist who appeared in the Doomed Megalapolis review) were going to do a skit where they charged at each other and ended up doing a You Are Already Dead moment. It didn't come together the way they wanted it to and it was cut.
Fax Headspace was originally supposed to have been achieved through prosthetics ala the original Max Headroom. The idea had too many moving parts and had to be scrapped, so they rendered him using CGI instead. Bill Rogers found the arrangement more favorable, seeing as he is a voice actor.