Litko can cut anything you want:
http://www.litko.net/categories/Bases-%26-Base-Bottoms/I just get the stock 20x40mm 20mil magnets and .8mm plywood. I think Hena may have gotten some custom ones from them with the holes pre-drilled too.
@jimmy - There are some issues that cropped up over the years:
- Magnetic sheet bases hop around on magnetic sheet lined trays. If you're using a metal case though that problem goes away. If you want to line trays with flex steel that'll be expensive.
- Magnets are stronger than plastic minis. Don't pick the base up by the mini, pry up the base and lift from there otherwise stuff breaks.
- 20mil is fine for infantry, for heavier vehicles or WM stands I'd go with the 30mil stuff for the extra strength.
- You can do this on the cheap with Evergreen Plastic sidewalk sheets (just score and snap) and the adhesive magnetic sheets you can get from Michaels/AC Moore (bring a coupon). It's more work but yields similar results. Just be aware that their magnetic sheet is weaker than the Litko 20mil stuff and drilling plastic needs to be done slowly or it'll melt.