It should. If not try changing the file extension to .M4V which is what Apple video playing apps like go see.
If that still doesn't get them to play there should be a menu option to "convert video to iPad", which should make an M4V copy with the correct aspect ratio and other encoding bits that will make it play nice with the iPads picky engine.
You can manually mange your iPads content. On the Summery (1st tab) of your iPad in iTunes is a check box that says " manually mange" this allows you to drag and drop content as you wish from your iTunes library into the iPad without syncing.
You can also use a number of 3rd party iPad apps such as GoodReader or FileBrowser and load movies into them and play them using the iPads video engine. You can even do so wirelessly. I know GoodReader can open/download files direcy from the internet if you give it the URL, something the native Apple built apps normally can't.