Due to being unemployed, I've actually had a chance to sit and play some emulated games more than a few minutes at a time. Quickly figured out that Dolphin Emulator doesn't support analog trigger buttons, so no Mario Sunshine. Ok, so lets play some Super Mario All-Stars using Snes9x EX+. Problem with that is that there is an increasing delay between button presses and on-screen action. After half an hour I can hit any of the buttons twice before Mario even responds. I've used the Shield Controler, a Moga 2 Pro, a wired Xbox 360 controller and a wired Logitech controller. They all start out fine, but after half an hour, games are unplayable because of the button delay.
Edit: Didn't think of this at first, but I have hooked my Ultrabook to the same TV and played Half Life 2 and Portal 2 on this same TV with no input lag issues and all the same settings on the TV as now. Any post processing this TV (LG 42LC7D) has that I can turn off has always been off.
Retroarch has been pretty great for me. No noticeable delay. I mostly play jrpgs though.
I did manage to play castlevania, sotn with it, and did not notice any delay.
Did you ensure your TV was in gaming mode?