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Your best bet for hard drives when building a new desktop is Serial Advanced Technology Attachment (SATA) drives. In the past two years SATA has become the standard for computer hard drives. These drives provide faster data transfer rates, thinner cables and better cooling efficiency than their predecessors (Parallel ATA).
New motherboards, even the most inexpensive ones, support SATA, so they will integrate perfectly with your new machine. If you are upgrading your hard drive on an older machine with a motherboard that does not have SATA connections, you will have to add an SATA controller card. You may also need a new power supply to support this move. For a short-term fix you could buy a second PATA drive to put in your system, but it makes more sense to upgrade all the way now rather than spend money on something you know you are going to have to replace soon.
Since it is going to be a few years before solid state drives reach the size and drop to the same price range as hard disk drives, SATA is the best way to go in the current market.