The basic connections would be as follows:
3 HDMI cables
Speaker wire
Coaxial 75 ohm RCA type cable for subwoofer
The PS3 and the Dish box connect to the Onkyo using HDMI. The third HDMI connects the Onkyo to the Samsung TV.
All the cables can be purchased at
www.monoprice.com
For HDMI runs shorter than 25 feet I like the High Speed HDMI 1.3a Category 2 Certified Cable 28AWG. The more expensive 24 gauge HDMI cable is not very flexible and should only be used when very long runs are required.
For the subwoofer, monoprice product id 3976 should work fine. Shorter cables are available if needed.
For speaker wire, monoprice product id 2820 should work fine.
This covers the BASIC required cables. Additional cables will be needed for the ethernet connections to the Onkyo and the PS3.
Hope this helps,
Ryebread