I have a Sony GT44IP. It cost me £130 last year, and was half price at the time. You can probably pick them up for like £70 now. It has Aux input and MP3 CD but also has an iPod cable which sticks out the back, you can plug an iPod in and control it from the fascia. It also has a remote control, for no good reason tbh.
As for subwoofers, no idea. Don't have one.
Do you know what you're doing? If you don't remember you'll also possibly need a fascia adapter and wire harness. For the subwoofer you'll need to run power cabling from the front of the car to the back. Etc, etc...