backup software for specific folders

With TM, you have the option of doing this, though you have to EXCLUDE the folders you DON'T want to backup.
But CarbonCopyCloner also gives you the option of a scheduled backup of specific folders.

 

Agreed! Carbon Copy Cloner! Love it.

 

you could set this up in Automator if you know how, I wouldnt be surprised if someone already did this and put it on the internet.

 

@seenew

Whether you are looking for a backup application which will automatically backup only the modifications since last backed up or just want to copy certain folders to other or external disk.

Just to copy certain folders to other disk you could accomplish this using shell script like the one mentioned in this URL

If you want to do the same using FREE application, then you could try StoreGrid to do unlimited local backups to your external disk for Free.