I happen to have some experience here.
I originally wired my family room with components from a company called JobSite. They offer nice components at a fair price. Their decora wallplate receiver is considerably cheaper than many other Plasma proof receivers on the market, and does a great job. Their website is:
jobsite
I think the whole system that I bought was less than $100, including the receiver, transmitter block, and one broadcast emitter that threw the IR signal to all of my devices (I have them on a shelf in my basement).
After awhile, though, I re-thought my strategy, and just bought an RF-enabled remote control from Universal Remotes. I bought the MX-900, and it is fabulous. I highly recommend this method if you can afford it. You can get the remote and the upgraded RF base station/IR emitter for around $350 at several places. More info can be attained (actually everything you'd ever want to know and more) at:
Welcome to Remote Central: Universal Remote Control Reviews & More!
I'm still looking for the name of the place where I bought mine, and I'll send you their name. Their prices are as good as anyone, and they have great customer service.
I might add that this solution, while seemingly expensive at first, is a long-term investment, not just in your HT system. A good universal remote, with RF capability, will open up many possibilities for you. Things like remote lighting, etc. Also, these things, particularly the MX-900 (or any of the high-end URC branded remotes) are amazing in their usefulness and flexibility. Macros, customized functionality, etc. I have mine controlling my TV in my family room, and all of my HT equipment (cable box, HT receiver, DVD player, HTPC) in my basement. Also my family room dimmable lights.
As far as running long distances of HDMI, I highly recommend checking out this site:
Home - FireFold
These guys are fantastic!! Exceptional prices on HDMI cables and accessories. They also know their stuff, so you can ask them technical questions. I bought a 50' HDMI cable from them for $75. That's right. 50 feet for approx. $6 more than Best Buy charges for a 6 footer. That's how much markup you get from BB and others like them on HDMI. In fact, Firefold sells a 6 foot HDMI for less than $5. And I, along with many of my friends, can vouch for the quality of their products.
Good luck with your implementation, and don't hesitate to ask if you have any follow-up questions.