Definitely CF. USB, SD Card and the like, they all have limits to how they can be used as permanent storage solutions without an IDE/SATA adapter; no UDMA; no support for true filesystems (currently CF can do JFS). CF is the alternative to SSD, SD (via reader) or USB are nowhere near.
http://bbs.archlinux.org/viewtopic.php?id=48524 - read lilsirecho's posts http://wiki.archlinux.org/index.php/Diskless_System - a good read too and http://soft.com.sg/forum/gear-computer-sw/55922-daw-ssd.html for some practical opinions on CF. Have you not experienced the difference since you have already been running CF? Or yet to try the thumbdrive route? It won't be bad (we already do it with Live USB distros with write support), but don't make it an alternative to hard disks.
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