As far as I'm aware, across the board the internals are entirely the same except for storage.
They should be the same, but be warned, 8gb is hardly enough for anything these days -- a lot of games and almost all videos are over 1gb, and even though it says it's 8gb there is only about 6.07gb usable.
Unless you're talking about getting an Apple Refurb model (which ships to you with a more up to date OS), the 8GB will likely come with iOS 5.x.x whereas the 16GB will definitely come with iOS 6. Mind you, it's not like most iPod touch users are dependent on having Google Maps and it's not like there isn't a free Google-supplied YouTube app to replace the one previously in iOS 5.1.1 and earlier. I'd go with the higher storage, you'd be surprised how small 8GB is on a modern iOS device.