I think I've mentioned these on the board before, but I highly recommend square plastic recessed bases. They're available from thewarstore.com (this product) in the US. They're actually Freebooter bases, so if you're in Europe you're probably better off getting them directly from them (includes a nice picture), what with shipping costs and everything.
Most Bones minis will fit right in there, and then you can add gel pumice or putty or whatnot to fill in the gaps before putting flocking on. I've done it with a number of DHL minis (metal ones), and I was extremely pleased with the results. I'm planning on doing it with quite a few of my Bones as it will make them a good bit more stable.
If you do need to trim the base a bit, that's trivial with Bones (more annoying with metal).