1)wood (MDF, whatelse?? What width?)
I would recommend just using wood as it's a small piece, anyways, and it provides for a sturdier panel. 3/4 is standard.
2)laminate such as formica (contact cement to stick)
Laminate is good, but expensive. A 2' X 2' square will run about 12$ at Home Depot. It's nice stuff, but pointless if you use a full overlay for your control panel. It's most useful if you don't plan on using much artwork and plexi because of its resilience.
3)any artwork (printed on what material? should I get the art laminated instead so no sticking to lexan/plexi?
As for the artwork, if you're doing a full control panel then don't bother with the formica at all (waste of money). If it's a full sheet just have it professionally printed at Kinko's. There are also guys here who can do it for you for a good price. If you're just using small pieces to decorate here and there just use photo paper or somethig that comes out well. Whatever the case, laminating the stuff is not necessary
4)Lexan/plexi (how thick?) (Screw it all into place, mounting bolts=1/4" wood bit)
For a control panel you're going to want to choose Lexan over plexi because it's so much easier to work with. I would recommend using the thinnest you can find. That's probably 1/8, but if you can find 1/16 that may be even better. The buttons actually do a really good job of holding the stuff down so you shouldn't need mounting bolts unless your buttons aren't so close to the edges of your control panel. Then I would recommend small carriage bolts because you don't want someone to be able to pull them up or knick themselves on the screw heads.
5)Drill holes for buttons etc. (Joystick holes=1 1/4" wood boring bit, buttons= 1 1/8" bit)
That size will suit you for the button holes. That size for a joystick hole, though, will be cutting it close. It may be what others us, but I would feel safer going with a slightly larger hole. Otherwise the joystick may knock around the top edge. If you were drilling metal I'd just use the same 1 1/4 hole as the buttons. But the thicker your control panel gets, the larger the hole at the top needs to be.
6)Install buttons, joystick etc.
Is it possible to have no bolts showing whether it be mounting bolts or joystick screws?
If you counter sink your bolt heads before you lay down your artwork you should be fine and you won't see the heads.
When I install T-molding (T-molding.com, using 1/16" slotting bit for router) will it make the wood to lexan/plexi look nice (cover it up)? What size T-molding do I need?
I never routed out my own groove so I couldn't tell you the size. Your t-molding should be the same thickness as your panel, though, whatever that happens to be. You may want to take into account that as you add laminate and lexan your control panel is going to get thicker so you may want to consider choosing your control panel and t-molding accordingly.