I've had a few questions coming in about how I photograph specimens, so I thought I'd share the top-secret method which, due to budgetary reasons, mostly consists of 2 lamps and a table.
Depending on the size and budget you have, some skulls may need a rest to sit properly. If you have the time and budget, the sky's the limit. If you have deadlines and no money, you can't beat a cheap piece of foam.
You have a snap a few shots and change as you go. For our purposes, having a warm and cool lamp on either side seems to make folks pretty happy. There's no wrong way to do it, really. The lamps are cheap-o little desk lamps you could find at any hardware store, and the bulbs are those swirly, CFL light bulbs that will run you $4-6 dollars at the same shop.
For overhead shots you may want an overhead camera tripod. You can build one, (Instructrutables) or you can get lucky and borrow a table with an arm as I do sometimes. Or you can tip-toe-hover over the subject as I have been known to do once in a while. As long as you can be steady and not interfere with the lighting, *whisper* they'll never know.
Hoover if you need to - and you will - away any dust. It will save you shame and photoshop later.
And that is how it usually goes. Go be brave and experiment! Cheers!