It's definitely possible, but I sort of doubt it since Telltale's trying to be taken more seriously as a developer.
Do you remember the trailer they had to announce their deal with Universal? They showed off clips from Sam and Max, TOMI, Wallace and Gromit, and even CSI...but no Strong Bad. I'm not sure why there was no mention of SBCG4AP, but if I was to wager a guess it's that developing a game based on a Web cartoon, even one as popular as Homestar Runner, doesn't look good on a game developer's resume. Even though Penny Arcade is about as mainstream as an Internet work can get, it'd probably have the same sort of perceived effect on Telltale's reputation.
I'd love if a Penny Arcade game happened, though. But what could it be about? (I'm assuming it wouldn't be a continuation of On the Rain-Slick Precipice of Darkness.)