I think the only thing you can realy do is partition around them.
Harddrives are suppose to automaticly detect and remap around bad sectors with something called "spare sectoring" were the manufacture automaticly set aside spare sectors that would all be used to cover up for bad sectors. This is normal to have some manufacturing defects and stuff like this, and that capability is built into the actual hardware itself.
So it's the hardware of the harddrive that is suppose to take care of bad sectors, all automaticly all without you or the OS's knowledge.
Bad sectors showing up constantly is a very bad bad sign for harddrive health...
However when you make your file system, if you use mkfs.ext3 with the "-c" option it should map out the bad blocks and it would be like they never existed.
mkfs.ext3 -c /dev/hd##
were hd## = your harddrive letter and partition number