Depends how you installed the apps. If you got them from the marketplace, you can just redownload them from Marketplace once you have upgraded your system. If you installed it by cab files, just put those cab files onto a microsd card or transfer them to your computer.
As a side note, if you want to backup your contacts, text messages, or the usuals, use PIM Backup 2.8:
http://www.dotfred.net/default.htm