Generally speaking, this is better done by spending the money on letting someone who knows how to do this type of thing make a recommendation for you and spend the time to put it together.
There are tons of different apps in the iTunes store that can't actually do everything, or do what they can do with a pretty cumbersome interface.
You can go to a Harmony or URC remote control, and that may not be a lot better.
I'm not really sure what exactly you want to do, other than have one remote to truly control everything you are throwing at it, which is a lot more difficult than it sounds when you have such a variety of equipment.
Generally, this is where top shelf control systems really shine. They are more expensive, by a good bit. Getting them programmed is also a good deal more expensive, but at the end of the day, they also work and can do what you want. iPod docks to get music and control it from any docked iPhone/Pad/Touch. A music server to play back music/videos. A single button to run the theater.
On the other hand, it really depends on how much gear is in your hteater, and if your 'stereo' is part of your 'home theater' and what your version of a 'home theater' is. If you are basically looking for one remote to control one room, then I would add a media server to your one room and get a URC remote control programmed up to run things.