Will I have to create separate Apple IDs for two iOS devices to message each other? I have one Apple ID that I use for both my iPhone and my wife's iPhone. In iOS5, if we want to message to each other using iMessage, will one of us need to create a separate AppleID? And if so, will that affect apps that we've downloaded to the device using the other Apple ID?
You don't have to create separate Apple ID's for the iPhone because iMessage also works by using the phone number. 

However if you have two wi-fi only iPad's or iPod touch's then you will just have to use separate e-mail address.