I would imagine they use Photoshop or some other such software and sprites that they either rip themselves or get off off Bulbapedia, etc.
They could also try dark magicks, but it's not feasible. There's just not enough cat blood for it. --- "Murder of the living is tragic, but murder of the idea is unforgivable." - Janus, speaker of the synod
They use the former as the sprite template and photoshop the latter's face and palette swap its colors. --- Other M is the One More Day of Metroid http://farm5.staticflickr.com/4014/5138578909_05b321131a_z.jpg
Those who make fusions take a few parts of some Pokemon and splice it with the Mew. It uses the color scheme of either Pokemon, and, to be honest, is hard to explain. I found a video that can explain better.
I use this for my own fusions. It's quite a nice little guide that gives some tips. It can be Photoshop, or even MS Paint. --- Pokemon SoulSilver FC: 1335 1407 6427 When Life gives you lemons, throw them back and demand cookies instead! -Official Sandslash of the PMD3 boards