Hi,
I take it you're trying to make a watchdog timer. I wouldn't use the HDD LED signal for that. First there might be a voltage issue (the signal probably isn't 5V), second hdd activity is not a good way of checking if a computer is stuck. A computer can run fine without HDD activity (for a while), and a computer that gets stuck during HDD activity may be blinking it HDD LED all the time.
Like the previous poster, I suggest you use a program that sends a heartbeat signal every now and then.
An easy way is to use the computers parallel port. It uses 5V signals (like the Arduino), and its fairly easy to program. If you use another port (if your computer doesn't have a parallel port), you can make an opto-coupler using an led, a photo-resistor and some black tape. That way you don't have to worry about voltage conversions etc. It also means you keep the electrical circuits separated, which might improve stability, and prevent accidental miswirings from frying your computer or arduino.
Using the built-in USB to serial converter may not be a good idea. It can be a bit "moody" every now and then, so you would reset a perfectly fine running computer.
Pieter