I prefer PC controls. Controllers make my hands feel all cramped.
I think many games require many different means of control. when I Emulate, I use either a ps2-styled pc gamepad, an NES styled Gamepad (retrobit), a PC joystick (MS Sidewinder, nice...) for sensitive analog controls, or, and this one's pretty cool, a RetroBit SNES controller that I rigged with parts from an Actual Snes Pad (the face and buttons..), to make an awesome realistic SNES controller, to play Japanese Roms with an actual (sort of...) SNES controller. My Sega Genesis has 3 different controllers, the original 3 button, a Performance 3 button, and a ProPad 6 SG... some games feel better with different controllers...
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I use a console controller on a PC. Even as my mouse. So yeah.
I use a laptop and am not big on using the touchpad.
I tell you it's hard for certain games using the controller, but I've created an Xpadder profile for like 20 things even RTS. It hurts when playing an FPS that relies on pure aiming with the mouse and no autolock stuff. I recently went through Doom 3 and it was rough especially against the flying heads.
After i first began emulating i can say that keyboard wins on controls only because you can customize it to your own finger positions (for those who don't like using the home row style finger placement).
Since i use the home row style finger placement ive found so many games to be alot easier to play like smash bros and any ds game (ive seen where the buttons are placed and i don't like).
However whenever it comes to button mashers and analog control games i have to go with controller.
Layin down enjoying the fun unleashing the power of the sun and capturing them all until I'm done.
Definitely have a usb and wireless mouse on stand by. I don't use it often but the scroll wheel is awesome. It offers a lot more control as well.
Now as for the original question, I prefer console control for the majority of rpgs. FPS I prefer keyboard and mouse as well as RTS. Sports games going to have to go with console control. But really I mean pc you can hook up anything.