First of all, Barebones systems are NOT necessarily SFF. Tom's wants you to associate the word "Barebones" with cubes because they're trying to promote cubes. The reason they're trying to promote cubes was outlined by Omid Rhamat (former chief editor) at one of his speaches (later outlined in an overview of the event), that is they're trying to promote systems with limited upgrade paths in order to increase the sales of hardware and boost the industry. Nice for the industry, bad for the consumer, they represent the industry, not the consumer!
For a desktop, slim towers are portable and take up less width (they're narrower). For a home theater, slim desktops take up less space and match the width of home theater components better (they're shorter and wider). Both configuration are available in Micro ATX, and can be had with either SFX (a truely standard small form factor) or PS/2 (full sized) ATX power supplies. Micro ATX supports 4 slots (normally 1 AGP and 3 PCI for performance boards), giving you a much wider upgrade path. And Micro ATX is a standard form factor, meaning you don't have to replace the system when the board is outdated (SFF relies on the Flex ATX form factor board, with limited selection).
I know, the cubes "look cool" in that they mimic the look of a $90 Wal-Mart mini home stereo, but there are nice looking Micro ATX cases that look like anything from a metal briefcase to a home theater receiver.
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