iTunes Sync iTunesMedia Folder , Apps take space

Hi.

Just got back my iPhone 5 (64gb) from apple, they replaced my screen and battery for free.
On to the issue, I noticed that iTunes syncs all my apps that I have on my iPhone onto my PC (windows 8) , in C:\Users\Ivan\Music\iTunes\iTunes Media , there is a folder named :Mobile Applications it has a size of 26gb.

So what I want help with is the following: I want my iPhone to only sync my podcasts, music etc and NOT my apps, why should I synch them? I can simply re-download any apps I want via the restore purchase option in the AppStore.

also, if I simply empty the Mobile Applications folder will that effect my iPhone when I synch it next time?

Finally, What is recommended: A) restore from iCloud or restore from PC backup?

Thank you!!!:apple: