Cross-drilling rotors is not a good idea due to the fact that you are removing metal.  By removing metal, you decrease heat retention by the rotors.  If the rotors become saturated by the extreme heat, the heat looks for other avenues to escape - typically into the brake pads and eventually to the brake fluid.  In extreme cases, the rotor will crack due to too much heat!  Drilled holes tend to crack radially.   Cross-drilled rotors ultimately end up being a purely cosmetic mod.

Excerpt taken from the February 2001 issue of Grassroots Motorsports magazine:
(Full copy of text can be seen here:

If you don't know what brake pad degassing is, the term describe the condition when inferior quality brake pad compounds vaporize due to extreme heat. This gas that is emitted by the brake pad tends to float the brake pad over the rotor face, causing reduced brake friction!

A relatively new treatment to brake rotors is cryo treating.  By chilling the metal material down to sub zero temperatures and then slowly controlling the rise in temps back to room temperature, the internal molecular matrix structure within the metal is realigned into a stronger material.  Typical cryo treated rotors tend to last several time as long versus non-treated rotors.  Although this doesn't increase brake performance, it does make for more mileage on a single set of rotors...

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