If the dialog offers a Transfer Purchases choice, use it. Otherwise cancel out of the dialog, right click on your iPad under the Devices lists to the left, and choose Transfer Purchases.
When it is done go to the Apps page at the top of the screen, make sure all you apps are present and check-marked. It's not a bad idea to go through all the other sync settings also and make sure you have them set the way you want before syncing. Also look at the way the apps are layed out on the screen on the Apps page. If they are out of order try another Transfer Purchases and/or a backup (found in the same place as Transfer Purchases).
Warning: If you have pictures in the Photos app they will be deleted at the first sycn. If you do not have copies of them elsewhere you should back them up before doing anything else. I find the app PhotoSync works well for this. Be aware the photos synced to the iPad have been optimized, and may not be the same quality as the originals.