I got a full CanaKit, which came with a plain black case (as well as a power supply, heat sinks, memory card, etc.)
I don't really care about the case as long as it works. The one thing extra I've bought for it is a power supply with a built-in power switch. Normally I just leave it running since the power draw is so low, but I don't like having to unplug the USB every time I need to switch it off and on again.
For the controller, I'm using it wirelessly. It's set up in the living room and the distance from the Pi to the couch is too long for a wired controller. Plus we have two little kids so they would definitely trip on the cord if I used it wired.
It requires a little tweaking to get it working correctly, and additionally the PS3 controller takes over the entire Bluetooth system so you can't use other BT devices at the same time. But the drivers are built into the current version of RetroPie, it's just a matter of enabling and configuring them. There's a guide on how to do so here: https://github.com/retropie/retropie...PS3-controller
Edit: apparently you can use other Bluetooth devices alongside a PS3 controller, but you have to disable the PS3 driver, connect all the other Bluetooth devices, then re-enable the PS3 driver. Only if using it wirelessly; I don't think anything is necessary if using it wired.