For VLC 2.03 (what I have) theres a setting you can adjust.
Go to the menu, then VLC -> Preferences, and by default it shows Basic settings. At the bottom left, click on Show All
From there, go to the Interface tab, expand it, go to Main Interfaces, expand, and click on macosx. Here you should see the option, last one is Black screens in fullscreen, also disable Use the native fullscreen mode on OS X Lion.
That should let you maximize on your second monitor and still operate on your primary. Not sure about iTunes, I don't really use it, but I doubt they have a workaround since it probably uses the default OSX Fullscreen, which sucks.