I'm assuming the OP meant traditional CF cards, which is what I use. I use mostly 256MByte, 1GByte, and 2GByte cards. I prefer FAT-32 for efficiency. I use these in PC104 format embedded systems and ICOP VortexDX boards. The ICOP boots off of USB, had a custom CF reader integrated into the custom computer. The PC104 WinSystems board comes with the CF reader built in. I also use Panasonic Toughbooks models CF-51 and CF-52, both can be configured to boot off the USB port- including the CF cards in a reader. My CF-52 now has a 512GByte Fat-32 SATA (not easy to do) drive that dual-boots DOS 7.1 (win98se realmode) and XP. Himem.sys gives DOS access to up to 3.4GBytes RAM, either booted off the hard-drive or the CF card.
WinSystems sells an industrial grade CF card pre-configured to boot for their systems. Using the HP utility provides a large cost-savings compared with the Winsystems cards. The latter are spec'd for high-temperature operation, but I did not require the full temperature range.