Apparently there was a deeper joke to implementing Tom Sawyer into the Missile Command episode of Chuck, because I was never aware of any particular popularity of that song with arcades.
Now that I think about it, I think Futurama had a similar gag...
Either way, I was a little young to remember arcades in their hay-day. However, I do remember the arcade in my mall at one point had the Ninja Turtles arcade game. My siblings and I played that every time. We also played the Simpsons Arcade game there, as well as at the skating rink. Any arcade I could find, I played Area 51. Unfortunately, they weren't very social places for me. In the skating rink, most of the kids were older, and at the mall my mom would hover over us, frightened from horror stories of children being abducted while left alone in an arcade.
I do wish arcades were around more, though. Even as an adult I feel like it would be a great opportunity to meet other people. I've been meaning to check out a place called University Pinball in Philadelphia, and I've heard word of a place called Barcade in Philly as well as NYC. So I think in some ways they're coming back, but not in small towns.
Which is the real shame of it. The suburbs literally have nothing for kids to do, and is where things like arcades are needed the most. Instead, you need to be able to drive 30 miles or so to the nearest mall or movie theater, rather than placing things within walking distance with sidewalks a plenty.
So next time people bitch about teen pregnancy and drug rates, well, ask them what else suburban kids have to do?