I cut plexiglass for my control panel top. I used a scroll saw blade (made for cutting through plastics) to cut the outline of my control panel top. I used a standard 1-1/8" wood bit to cut out the holes (make sure the holes are cut 90 degrees so the actual pushbuttons will fit into them straight). I went real slow and it worked real well.
I was worried about cracking as well, so I sandwiched my plexiglass between two 3/4" MDF pieces of wood before cutting. Basically, I made my control panel top out of 3/4" MDF and cut/drilled everything out of it. To set up for cutting my plexiglass, I placed spare 3/4" MDF board on my workbench (ie: bottom piece), then placed the plexiglass on that and taped the plexiglass down which a lot of blue painter's tape all the way around to make sure it would not move at all. I then placed my 3/4" MDF control panel top (which already had all the holes, etc... cut in it) on top. I then clamped both MDF (bottom and top) together (with the plexi in the middle). I made sure to clamp to the left and right side of where I was going to cut/drill so there was always a nice firm "sandwich" created. Finally I used my top control panel MDF panel as a guide to cutting out the holes and trackball space, etc... It was nice since the button holes already drilled out of the top MDF piece guided the drill bit correctly into the plexiglass. Basically, it made sure the drill bit was cutting into the plexi at a 90 degree angle. The bottom piece of MDF was basically scrap and was thrown away when i was done.
The more you speed up, the more chance of cracking. I would try to get spare piece of plexiglass to practice on. Once you do it, you will understand what needs to happen in order to cut nicely.
I believe the idea with cutting plexiglass (or lexan) is that you really do not want to "cut" right through the plastic as if it were wood (ie: do not push your scroll saw blade through the plastic with a lot of force). Instead you want the moving blade (or drill bit) to heat up the plastic befoer trying to apply more pressure to make it cut through. For example, cutting a 1-1/8" hole for a button you would not just place your drill bit at the desired location and start pressing down and drilling right through the plastic, but rather you would allow the little point of the drill bit to spin in place a bit, thus heating up the plastic . You would then push down until more of the drill bit goes through the plastic and then wait for more of the plastic to heat up a bit and then continuing pushing down, etc, etc .... until you are all the way through.
** Plexiglass and lexan usually come with a thin protective film applied to it to keep it from getting scratched when it is stored with a bunch of other pieces. I would "highly recommend" you keep this protective film on the plexiglass until you are done cutting everything. It obviously will protect your plexiglass when your cutting but it also seems to reduce (a bit) the amount of cracking which might occur (if any).
So to recap:
1) Practice on some scrap first (if possible).
2) keep protective film on plexiglass
3) sandwich plexiglass between your true control panel top and some scrap to use as a guide
4) Cut/drill slowly so plexiglass melts as it cuts