The basic, foolproof, guide is: If you're buying a Genesis get a Model 1 with the EXP port on the back. If you're getting a Japanese Mega Drive get one with the text 'AV Intelligent Terminal' 'High Grade Multipurpose Use' on it. Don't buy a PAL one. If you want to fuss over details and try to get a bargain check the guides linked.
Controller selection is pretty boring!
The best standard pad to get is the official six-button controller. I don't like the three-button controller, but it feels weird playing a Mega Drive without one. Haven't tried any third-party ones, but have heard good things about the SG Propad (SNES-like) and the Tetsujin controller (red/blue/purple buttons). Hori do a Mega Commander pad.
For joysticks there aren't many options. The Japanese versions of the official sticks (Arcade Power Stick) are decent, the non Japanese versions don't have microswitches. There's a version of the Capcom Power Stick Fighter, but it's pretty pricey. The colours are nice.
There are some famous Micomsoft controllers, their two variations on analogue controllers the XE-1AP and XE-1AJ. The XE-1ST2 and XE-1SG should work(?), but they're only three buttons anyway.