If its pirated, or CoD or GTA or other computer games that is not available at the App Store you can't transfer it. In fact you can't transfer
Apps from your computer to your iPad at all.
If you have purchased them using the Apple ID your using in your computer and you use that Apple ID in your iPad you can download it in your iPad by going to the App Store-> Purchased and there you can find all the stuff your purchased in your computer (Of course the ones you downloaded in iTunes).
Of course, there may be apps there that is not listed in your iPad cause they are not compatible for iPad........