Two of my Onkyo HTIB setups have Ipod docks that allow you to control the Ipod with the remote.
In the bedroom, we each use the iHome iP9. It's convenient to just put our phones on them when we go to bed, so they will be charged every morning. They are pretty badass alarm clocks as well. You can wake up to radio, buzzer, random Ipod/Iphone shit, or a dedicated iHome playlist that you set up. The songs (or radio or buzzer) start out soft and gradually get louder. It's a much nicer way of waking up than the ol' Aeh Aeh Aeh bullshit. I wake up most mornings, pissed to be awake, but then I say "Damn, that's a good song!" They are usually $80-$100.
Then we also have this portable, weatherproof thing that we can take anywhere. It's badass. Not sure what it's called, but I got it at Sears when Leah posted it up in one of her "deals of the day" threads. My only regret is that I didn't buy one or two more. It rocks. Not sure what the brand is, and I am too lazy to go look right now. It was a steal at $50, but I think they are normally $100 or more. If you want something you can lug around anywhere, this is it. No clock though, and no remote.
James has a dock in the garage that has a clock too. It looks like an old fashioned radio. Doesn't get crazy loud, but it's cool, and has a remote and all that jazz. I thin it has some aux inputs for other plug in shit as well. Maybe even a USB slot. Not certain. I bet it was under $100.
I'd have a hard time spending too much on the fancy docks, because you might as well get a stereo or htib system with a dock and get as loud as you want. As for sound quality, you can only get so good with an Ipod anyway. Bleh. Like cooking a cheap sirloin on a badass grill.