"I want to use that template that SNAAAKE pointed me to, but I'm having a problem deciding what color buttons to order. I saw some project that used the "Neogeo" color scheme, and I thought that looked nice. The only problem is that I forgot where the site was. Does anyone know the colors and order I'm looking for?"
I'm going straight black for all the buttons except for the coin and start buttons, which are green and white respectively. Use whatever YOU think will look best with the cabinets. Just keep in mind what you want someone looking at; the buttons, or the artwork underneath.
If you're going to have labels on all of your buttons (Like SFII cabs had for example), and a "compass" around the joystick, then I would suggest multi-colored buttons. Otherwise I'd pick one color that blends in more with your cp picture so the controls don't stick out like a sore thumb. That's only my opinion though..
"Also, it seems to be quite popular to cover artwork with plexiglass."
Lexan would be a better way to go...Plexi has a tendancy to crack and chip when you try to drill through it, and it's not as resistant to physical abuse as much as Lexan is. Sounds anal retentive with the correction, but there is a big difference between the two.
"First of all, how do you get that artwork on there in the first place? Is it just a printout from a normal printer?"
I'm looking at getting the side art for my cab here...
http://www.angelfire.com/clone/mameart/...and making my own CP overlay and marquee and printing those at Kinkos. I'm going to make the picture a bit larger than the control panel, and just trim it down to size with a knife once I have it in place. Since I don't have any artwork or text that has to line up with any of the controls, it's not going to look odd if it's slightly off square (Although I'm going to attempt to put it on straight of course).

"Do you just glue it on afterwards?"
Since it's just high-quality printer paper, I'm just going to use some spray adhesive to hold the paper in place, then screw the lexan sheet overtop to anchor it. I suppose glue would work, but glue and rubber cement won't hold paper to wood or metal very well, and they have a tendancy to wrinkle paper from the moisture in the glue. IMO it's the Lexan overlay that really holds the picture in place, the spray adhesive is just there to keep it from moving around while your working with the cp and Lexan.
"Secondly, after covering a controller with plexiglass, doesn't that mean the joystick will end up being much much shorter? How do you get around this? I know routing works, but is that the only way? I want to try and avoid that."
Only 1/8" shorter than it would be without the Lexan. Using a router on the underside would be the only way to make up the difference. I'm not sure arcade cabinets with lexan overlays do this, so it might end up actually being taller than a "real arcade cabinet." I'll have to talk to a friend that works at a local arcade to see if I can take a peek at the underside of a panel and see.