The best file is a gerber file with embedded apertures (RS-274X) of your stencil layer (also called paste or cream layers). The stencil layer is NOT a solder mask layer (typically the green insulator on a PCB), which has expanded apertures and includes through-hole pads and vias. If your software does not support a stencil layer, you can make a copy of your design and delete all the copper except for your pads and then send me a gerber of that layer.
If you have multiple designs you want to submit at once, please send them in a single .zip file.
A real dedicated site for the stencils is coming, but for now, we have some basic information at http://www.SMTstencil.com, and you can email your file directly to me at jan at this domain.