Cartoon Network's new show, Regular Show has a SEGA Master System as a plot device. It's seen throughout the entire episode, but you only really get a good shot of it :32 seconds in.
There's also House of Pain's "Jump Around" with the lyrics: "Try to play me out like, as if my name was Sega" at 2:19
In Futurama's "Spanish Fry" episode, Prof. Farnsworth exclaims, "What in the SEGA Genesis happened to you?" to Fry. I can't provide a clip, due to there not being one.
I'd love to see the contributions that the rest of you have, gogogo.