So since it seems like nobody wants to contribute, I'll start with a list of things to try to get rid of engine whine.
First, and probably most common, is GROUNDS. Check all grounds for good connections. Always have the most solid and direct ground connection possible.
Second, check your RCA's! Some RCA's have screwed on connectors that can come loose and cause problems. Also, make sure your wires arent getting pinched bad anywhere. Also, its a good idea to route RCA's away from power/ground wires. Anything that could cause interference to pick up. It would also make sense to use a good quality RCA, but I cant back that up because Ive had good luck with "cheap" RCA's and have had some bad luck with more costly "brand name" RCA's.
Third. Check your equipment! I had a side plate come loose on an amp one time (probably from vibration) and it was contacting the RCA terminals of the amp and caused all sorts of noises. I thought I blew the amp up! Found and tightened all screws and problem went away.
Fourth. ----FEEL FREE TO CONTRIBUTE PLEASE!!----
KEEP THIS GOING!!! ITS STICKIED!