Preferably, this would be a computer connected via cable, but if there's a way to do it over wifi then this would also be useful. I'm wondering if it's possible to send messages between them?
Or if i had a mac app and an iPhone app, could I communicate between them over wifi or a usb connection, rather than using a server or something?
Connecting over WiFi is possible, cable connection however isn't possible (certainly not in the documented API) unless the phone is jailbroken.
For wifi you're just going to connect to a TCP/IP host/socket. Have a look at CocoaAsyncSocket. The computer would need to be hosting some sort of server software. This is how iTunes Remote and AirMouse work.
There are some "permitted" (non-cracked phone) ways to send data to the iPhone from a device that's physically plugged in. There are several barcode readers - like the Linēa-pro used in US Apple stores - and magstripe readers for credit cards (e.g., the Macally Quikswipe) that can send limited amounts of data to/from the iPhone.
If your computer is a small embedded device and your data requirements are meager, it may be possible.
