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Should you buy a desktop or tower case? Our advice is go with tower unless you're building a no-expansions personal system and expect to be using the floppies a lot. Many vendors charge nothing extra for a tower case and the absolute maximum premium I've seen is $100. What you get for that is less desktop clutter, more and bigger bays for expansion, and often (perhaps most importantly) a beefed-up power-supply and fan. Putting the box and its fan under a table is good for maybe 5db off the effective noise level, too. Airflow is also an issue; if the peripheral bays are less cramped, you get better cooling. Be prepared to buy extension cables for your keyboard and monitor, though; vendors almost never include enough flex.
The airflow thing is a good argument for a full- or mid-tower rather than the `baby tower' cases some vendors offer. However, smaller towers are getting more attractive as boards and devices shrink and more functions migrate onto the motherboard. A state of the art system, with all 3" disks, 200W power supply, half-size motherboard, on-board IDE and 64meg of RAM sockets, and half-sized expansion cards, will fit into a baby or midized tower with ample room for expansion; and the whole thing will fit under a desk and make less noise than a classic tower.
For users with really heavy expansibility requirements, rackmount PC cases do exist (ask prospective vendors). Typically a rackmount case will have pretty much the same functionality as an ordinary PC case. But, you can then buy drive racks (complete with power supply), etc. to expand into. Also, you can buy passive backplanes with up to 20 or so slots. You can either put a CPU card in one of the slots, or connect it to an ordinary motherboard through one of the slots.