Under the Store menu in iTunes, make sure your computer is authorized. At the top right, make sure you are logged into the store with the same account that you use on the iPad. If by chance you were logged into another account, hold in mind that any app purchased under another account and synced to your iPad will not update on the iPad unless you also chance it's account invthe store.
With the iPad connected, select it under the Devices list, go to the Apps section at the top. Make sure that you have app syncing turned on, and that all the apps you want on the iPad have checkmarks next to them.
If you have apps on the iPad that are not in iTunes, right click on the device and choose Transfer Purchases. Do this be for you sync or turn on App Syncing.