Stopped by one of the Good Wills that I don't regularly go to and they had a boxed Super Nintendo... They wanted $319.99 for it. Rips and wear on the cardboard, my guess is it wasn't actually new.
They also had a $9.99 GameCube that looked like they actually pulled it out of a mud puddle and the dirtiest Xbox I've ever seen for $25.99, no cords or controllers, just the console.
Some of these idiotic managers at the Good Wills in my area need to stop relying on eBay to price things, not to mention they need to learn to take into account condition of things when pricing them.
I see the same crap most of the times I go to Goodwill, as well. In the event that they even have a system for sale, it is generally priced at or above ebay prices. It is also generally dirty, and missing wires or something else. I get that they want to make some money off of it, but they need to keep in mind that people shop there for good deals. Same mentality that I see once in awhile when I see some old gaming system (generally an NES or SNES) at a yard sale being sold by some old woman. It's automatically worth $100 because one sold for that online.
Of course, pricing varies by location. Best to find a location that prices decently. I tend to rarely shop Goodwills, and try to frequent privately owned, for-profit thrift stores that get their goods from other means besides donations (but still charge fair enough prices). It tends to bring in a higher quality of goods, both games and otherwise.