I prefer going the mSATA route over CF cards.
My reasons are two fold:
1. CF media is designed basically to be written to, read, erased, and start the whole thing again. Using it as system's main disk is going to involve a lot of random access and other things that CF cards aren't really designed to do. They can work well for a while, but really don't have the duty cycle design for a system disk
2. CF cards are expensive vs. mSATA SSDs in similar capacities.
So, not only are you paying more for a CF card, you're getting what really is an inferior technology in the sense that the mSATA is really designed for what you're using it for.
I think part of the attraction of CF cards is that they can be had in capacities much lower than typical mSATA drives, which can make them an economical option esp. if you're dealing with a computer that shipped with a 10gb or smaller HDD. With that said, though, for relatively modern computers like the Cube and especially late Powerbooks(where I've used a lot of mSATA drives), the benefits of an mSATA drive are there.