Which would better suited for a CNC drilling machine: gerber or gcode?

Gerber files are used for making boards, not for CNC drilling. Drilling requires Excellon drill files. Excellon drill files can be generated by Eagle, and would be be more convenient for users than any other format, as no file conversion would be required. They are quite simple.

I agree with Leon - I didn't even know where was a choice. I thought all CNC machines relied on gcode. I know of gerber to gcode converters: http://sourceforge.net/projects/gerbertogcode/

I dont' know about the appropriate drill converter or even if you need one. I think Leon's right about the excellon drill files.

Sounds like a cool project. The standard format for a drilling machine to accept is "Excellon file" format.

Most CNC machines accept

• a G-code that is a slightly enhanced dialect of RS274D.

Most PCB design software exports information about a file in two formats:

• drill files in "Excellon file" format, a variant of standard RS-274C. (This is the one you want).
• layer files in Gerber file format, a variant of of RS-274X.

All three variants of RS-274 are very similar.