Yes.
You download appsync from cydia, then you can either go to apptrackr.org and download them like mp3 (apps are .ipa files though), put them into iTunes and sync like normal. Second option is to also download installous from cydia and download them straight from the device like you would with the app store.
Are you jailbroken already? If not follow the links for help. The first will tell you how with links to files you need, and a guide. The second just has more info on jailbreaking.
http://jailbreakmatrix.com/iPhone-iTouch-Jailbreak
http://gizmodo.com/5533921/how-to-jailbreak-any-iphone-ipod-touch-or-ipad
Other useful sites
Modmyi.com
Funkyspacemonkey.com
Cultofmac.com