It's probably just the heads parking when the drive goes into powersave mode.
I know exactly the sound you're talking about and its g-damn annoying. I just took the 320 WD Cav Blk drive out of my MBP and replaced it with a 500 Seagate 5400.6 and lack of 2 minute clicking is a relief.
You should definitely run the SMART utility, but drive failure ticking is usually a little more frequent than every couple of minutes.
Good luck,
John