There are a few things I'd like to note... (assuming you have a desktop)
To check if the sound is your HD, disconnect the power cord from your HD and start your computer. If the sounds is not present, it was most likely the HD. If it is still present, I would say case fan or CPU fan. My system does the same thing, reboots do not recreate the sound because the fans never stop spinning.
With the addition of the HD LED problem, if it started at the same time as the sound, I fear the worst and your HD is dying.
Honestly, I have no advice for the LED problem if it is not the HD. Remove the wire from the Mobo and put it back on. If that does not solve the problem, and it bugs you... disconnect it entirely.
If it is your harddrive, replace it as soon as humanly possible. If you have to wait due to budget for any length, backup your important files on removable storage now.
If you believe it to be the CPU fan, and cleaning doesn't help, I would suggest replacing the fan if you have the funds and know-how. It may be unnecessary, but the CPU is a rather key component and heat is a bad thing for it.
No matter what I suggest cleaning the dust from your computer regularly. I have an acrylic case with 5 case fans.... it gets dusty fast and you can see right through the case. But that dust builds up in the fans creating a heat and (however unlikely) fire hazard.
If I can help any more, let me know... and if anyone reads this and disagrees, post your opinion... I have no problem being corrected especially if someone else's system might be affected.