Tools I've used that are helpful:
- displays the usual S.M.A.R.T. statistics
- Available on many Linux LiveCDs, such as Trinity Rescue CD, and....
Not available on: Knoppix v6.x, ...
- lets you have pretty fine-grained control over disk-initialization and spin-up, to try to determine what's wrong
- Available on: HawkPE (probably many others)