Also: Since you're doing this with a PDA, you'll need to find something that lets your PDA send out the "magic packet" that wakes up a machine when it is sleeping. Perhaps there is a tool for your particular PDA OS (PocketPC, PalmOS), or perhaps you can get a perl interpreter.
It would likely be easier to leave the machine always awake, and, if conserving energy is the goal, set the monitor to sleep and the hard disk to spin down. The machine is always ready for use, but is consuming very little power. If, on the other hand, paranoia is at work (i.e., "evil h4xx0rs will get me"), then knock yourself out.