My suspects in order would be:
- Power Supply
- Fan
- HD
If possible I'd start with opening it while it's running and try to isolate an area. The fans are hot swappable as are the power supplies if you have duals. If it seems to be one of those, pull them until you find the culprit. If it's a fan, you now have a new desk toy. Seriously. I wouldn't even bother replacing it. There's something like a dozen in that box. If it's the power supply, ebay is your friend. HD, give it a shiny new SSD.
I don't personally subscribe to "shoot it because it's old." If it is doing what you want in the way you want then keep it. Too much electronics in landfills as it is.