You can't fix physical bad sectors and must remap to avoid them and this is
low level and tedious. You can do it from Linux or Windows but must work
from an unmounted partition or drive. There are utilities that you can
download or use ones that come with drives which are the best tools for
this, IMO. You can fix bad logical bad sectors which are software based, but
you should find out which they are first. There is a good discussion here
and some tools that you might use:
ask.metafilter.com/.../How-best-to-respond-to-a-bad-sector

What hard drive/model do you have? How old is it?

Depending on the firmware on you hdd, it may have the technology to
automatically retire bad sectors and mark them for non-use. Most new hard
drives have diagnostic firmware that detects when the hard drive is failing in
several different modes.

Other than that, the fsck command as has already been pointed out is a good
place to start.

You can also download the hard drive manufacturer's diagnotic software to check
out your disk.

Depending on what the model of your computer. When you boot your system, please
go into BIOS. Some versions of BIOS will test your HD for fail parts. Not only
that. Test your RAM and CPU. Now I must ask why you think it may be the HD?
What is your system doing that you do not like?

On 10.04,9.10,9.04 and I don't know how far back, the system
automatically tests the condition of the hard drive on startup after a
set number of boot ups. Disk utility under administration>system> "disk
utility" will run the diagnostic and tell you the condition of your hard
drive and if you system has the ability temp and other information.
Ubuntu ain't MS, it is so much more. You can quit looking for utilities
that keep Windows working and expect that much of the work of keeping
the system in top condition works automatically under the hood.