I am looking for a remote control that can:

1. Control DirecTV receivers using native RF
2. Has RF to IR for other components
3. Has Addressable RF to IR to control Components

My setup in my Media Room:

1. 3 Samsung TV's that use the same IR remote control (want the universal remote to route the IR to the correct TV)
2. 3 DirecTV receivers - using RF Remote Control
3. Onkyo TX-NR906 Receiver
4. HDMI 4x4 Selector
5. Mac Mini

I would prefer a remote that I can program, but willing to go the professional route.

The only universal remotes that control a directv receiver via RF directly are the Acoustic Research xsight Arrx18G, and Nevo C3. no others.

And they can only control one RF Directv receiver at a time.

Thanks. If this is the case, then my desired solution doesn't exist. This means that I would need a RF-IR Remote that has at least 7 addressable RF-IR Zones. Any ideas?

and can only use one base in a house as well as no IR routing on the RF base

Without understanding what exactly you are trying to accomplish a recommendation is a bit hard but I can tell you that most anything in the URC professional line can do this. I believe all of the current generation pronto's can do this. The Nevo Q50/S70 should be able to do this as well.

Pretty much any remote supporting addressable base stations and configurable IR/RF routing. How many base stations you will need depends on what you are trying to do and how the room is configured. Emitters can be split as long as you don't send them both to the same kind of device.