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In deciding what style case you want your system to have, there is one decision you generally need to consider first: where you want to put it. You generally have two choices here: on the desk or on the floor. Putting the case on the floor gets it off your desk, saving desk space. However, it also means that the power and reset buttons, the indicator LEDs, and the drives, are less accessible to your fingers, and more accessible to accidents involving your feet. This is in some ways, the biggest drawback of a tower case. In some cases you will need cable extenders for your keyboard, mouse or monitor, depending on your setup. Also, if you are getting a smaller-sized monitor, say 15", you may need something to put under it so that it is at a comfortable reading level (larger monitors usually work better on the desktop directly). Finally, there's the chance the box will get kicked or knocked over, or you'll hit the power switch with your knee at the worst possible moment (Murphy's Law--ignore it at your peril!)
A tower case is generally recommended for a floor location, for stability. You can put a desktop on the floor, on its side, as long as you secure it properly (you don't want the box falling over!) If you do go with a desktop on the floor, some companies sell (used to sell?) brackets intended to support desktops put on their side; you may still be able to find one of these. A desktop case is of course better for putting the machine on the desk; a tower case can be put on the desktop but it will take twice as much room since the monitor can sit on top of a desktop case but not a tower.
Note: There are apparently some
types of cases that can be "converted" from desktop to tower and back again by
changing their front panel. You may need to
purchase additional hardware in order to make the change however.
One final consideration is the orientation of your drives, in particular CD-ROM drives, DVD drives, and other removable media. Many of these drives will not tolerate being mounted on their side, which means you need to consider how the system will be oriented in advance. Most modern hard drives will operate just fine mounted either vertically or horizontally.
Next: Full Tower Case