There's nothing funny about the Penny Arcade strip. It's just mean.
No... Gabe is being mean. He's being a total asshole. He's going off on a huge alpha geek tirade about something inconsequential. It's making fun of him, and all those who would completely overreact and fly off the handle about something that really doesn't matter, like having a 0 in front of a registration number, NCC-0514 vrs NCC-514.