Because you have installed Cyanogen ROM you probably have a custom recovery installed such as CM-Recovery-1.4. Boot into recovery, you will see an option for backup, then place the SD card into your card reader. Copy the Nandroid directory from the flash card root directory. When you get your new card simply copy that folder back to the newly formatted (fat32) card, go back into recovery and use the restore from backup feature. Reboot.
BTW, just like when you flashed the rom, use Power+Home while booting up to get into the recovery console.
As long as you are not using apps2sd, this should fully backup and restore the applications.
You could also maybe get away with just copying the files from one flash drive to another and then rebooting, but file permissions might be all messed up - that I am not sure of.