Backing up certain folders

Time machine is not very suitable for this. By default it backs up everything and you need to manually add every folder you don't want to be backed up to its exclusion list in TM system preferences->options. If you only want to back up a few folders you might want to consider a different backup solution.

Basic Backup

Get an external Firewire drive at least equal in size to the internal hard drive and make (and maintain) a bootable clone/backup. You can make a bootable clone using the Restore option of Disk Utility. You can also make and maintain clones with good backup software. My personal recommendations are (order is not significant):

1. Retrospect Desktop (Commercial - not yet universal binary)
2. Synchronize! Pro X (Commercial)
3. Synk (Backup, Standard, or Pro)
4. Deja Vu (Shareware)
5. Carbon Copy Cloner (Donationware)
6. SuperDuper! (Commercial)
7. Intego Personal Backup (Commercial)
8. Data Backup (Commercial)

The following utilities can also be used for backup, but cannot create bootable clones:

1. Backup (requires a .Mac account with Apple both to get the software and to use it.)
2. Toast
3. Impression
4. arRSync

Apple's Backup is a full backup tool capable of also backing up across multiple media such as CD/DVD. However, it cannot create bootable backups. It is primarily an "archiving" utility as are the other two.

Impression and Toast are disk image based backups, only. Particularly useful if you need to backup to CD/DVD across multiple media.

Visit The XLab FAQs and read the FAQs on maintenance, optimization, virus protection, and backup and restore. Also read How to Back Up and Restore Your Files.

Although you can buy a complete FireWire drive system, you can also put one together if you are so inclined. It's relatively easy and only requires a Phillips head screwdriver (typically.) You can purchase hard drives separately. This gives you an opportunity to shop for the best prices on a hard drive of your choice. Reliable brands include Seagate, Hitachi, Western Digital, Toshiba, and Fujitsu. You can find reviews and benchmarks on many drives at Storage Review.

Enclosures for FireWire and USB are readily available. You can find only FireWire enclosures, only USB enclosures, and enclosures that feature multiple ports. I would stress getting enclosures that use the Oxford chipsets (911, 921, 922, for example.) You can find enclosures at places such as;

Cool Drives
OWC
WiebeTech
Firewire Direct
California Drives
NewEgg

All you need do is remove a case cover, mount the hard drive in the enclosure and connect the cables, then re-attach the case cover. Usually the only tool required is a small or medium Phillips screwdriver.

Graiai wrote:
I only want to back up certain folders. How do I do this with Time Machine?

As VK noted, TM is not really a good solution for your needs.
You might consider manually backing up the files by copying them, writing a simple script to do it and run it occasionally, or just before shutting down the system.