I play on the PC. I'm still playing Madden 2005 because I can still download plenty of updates and rosters. I think the graphics are a lot better on a PC, if you have a graphics card. I've always preferred the PC version, you can do so much more tweaking to the game and the teams and there are unlimited roster updated and possibilities. Gameplay is still fun too.
I have a Gravis Eliminator controller. I love it. The directional controller is a ball and that makes it VERY smooth and precise. It's the best controller I've ever used. It's especially good for Madden and NBA Live, you can make some amazing cuts (Portis!) with this controller and it's really confortable to hold with rubber on the bottom. See if they have one at Circuit City and try out the display model, you'll love it.
eBay: Gravis Eliminator Gamepad Pro PC Controller (item 150120095937 end time May-13-07 17:43:02 PDT)
If you want the hit-stick controls on newer Madden, just pick up a cheap PS1-PS2 controller and get this USB adapter from Radio Shack to use it on your computer. I use a Playstation controller on my PC for MLB '06 because it requires the extra sticks to play.
RadioShack.com - Toys & Games: Accessories: Video game accessories: Cables, adapters & switches: USB Adapter for PlayStation®2 Controller
eBay: MadCatz Mad Catz Dual Force 2 Controller PS2 Blue Mint (item 300095590529 end time May-25-07 16:01:59 PDT)
I have one like this. $10 at WAL*MART.