I've heard it mentioned elsewhere, one cannot programmattically hook into the phone call area of an iPhone using the current SDK. I'm looking to learn iPhone development and Obj C, with the end goal of creating a call timer app that runs in the background and alerts the user when a call has gone on too long.
Is it even possible to hook into methods liek that?
No. Your app will be interrupted when the user receives a call, and your code will not be allowed to run while the user is on the call. Additionally, there are no background apps allowed for the iphone. The best you can get is push notification, but you can't create a daemon or anything like that.
This information is provided in the iPhone Application Programming Guide