How can I enable synch without losing my apps?

Hello,
I read the forums and I cannot find a solution to my unique situation.
I have a 2nd gen iPod Touch and synced apps and music with iTunes and everything was mostly great. The only problem was the slowness of iTunes so I started using MediaMonkey instead to transfer music. I also downloaded apps exclusively through wifi, so I never bothered to sync my iPod with iTunes for months. Then I upgraded the harddrive, did a clean install of Windows, and sold my old harddrive. It was not possible to sync my iPod anymore and I didn't care because MediaMonkey/Wifi worked perfectly for my needs ...
Until I installed firmware 3.1! Now MediaMonkey crashes and I can't add/remove songs from my iPod. So I was going to wipe my iPod and give the new version of iTunes another try, but now I am worried about losing all the apps I've downloaded over wifi. I've logged into iTunes and I cannot find a record of apps that I have downloaded/purchased. *Which brings me to my question: How can I enable synch without losing my apps?* I'm particularly worried about the apps that were free when I got them but they now cost money.
Thank you for your time,
bougatsa

The "File -> Transfer Purchases" option didnt work at first, but then I clicked around and managed to get this new computer image added to the new Home Sharing feature. Now all my iPod apps have been transferred to my local iTunes apps folder, thank you Julian!
And Anna, thank you (tack?), I believe you that it works but now that I have my apps locally I won't try I'm sure you'll understand.
I had bad thoughts of ditching my iPod for something else but I won't now! This forum rocks! Thank you all again
Bougatsa

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