Your question is less about "I have a problem and want to fix it." versus, "I don't want any problems in the first place. What are the best practices to follow?"

Literally the only interference problem I have every had was a vario that deflected when I keyed the transceiver. Solution: replace the vario. I must live a blessed life. This has also been in pure gliders only so I don't have to worry about ignition noise which is by far the worse culprit for interference. However, new electronics run at some high frequencies (1Mhz processors are sloooow these days), so interference can happen.

So back to what I do to prevent problems in the first place.

1) Start with QUALITY - Components, wiring, terminals, switches, etc. Buy from an aviation source like Wicks or Aircraft Spruce. Radio Shack and ACE Hardware DO NOT have aviation aisles. Modern avionics seldom seem to create issues as they have to pass some pretty stringent testing to be certified. Step away from anything still using crystals (are they still legal?).
2) Coax for microphones and antennas. But every microphone and antenna already comes with coax. The more important bit is making sure that the shield has a good ground at the avionics end. A good BNC connection for the antenna (have someone knowledgeable help). Many transceivers have a separate ground pin for the microphone - use it!
3) Ferrite beads - While my EE specialty is not in the RF spectrum (get it?), putting these on doesn't hurt and might help ... so I use them. As someone in this thread said, run both the +/- wires through the bead twice if you have the slack. Non-split beads are generally better than split beads. The trick is to prevent high frequency noise from one device getting into another device through your power bus.
4) Air gaps - Wires that might have data flowing through them, like a GPS to a PDA, can induce noise into another wire running right along side of it in a bundle. So separate any suspect wires from one another.
5) Grounding - Ground all your devices to a single common location as close to the electronics as possible, including the negative side of the battery.. Even ground the metal stick, push tubes, etc, if possible.

Good luck, John