I am lucky enough to have a source for caustic that I use every third brew (PBW after the other two) to clean up things like pumps, plate chillers, and conicasl since it kills everything organic. That said I take apart the ball valve on my fermenter occasionally and inspect the insides to be sure that there is nothing lurking there (I have the ones that allow you to do that). I started doing this after Jamil mentioned doing that at a Homebrew Con a few years back.
Boiling them is a good idea but taking them apart will reveal anything that boiling may not have gotten rid of. If you can't take the valves apart then boiling or use of caustic (be very careful if you use it, gloves and goggles are a must to protect yourself from burns) will help alleviate this issue.
SS Brewtech also recommends passivating your stainless at least once per year. They recommend one ounce of Star San in a gallon of water to get rid of any beer stone that may have accumulated in the vessel which can harbor nasties. Use a sponge to coat the sides with the mixture several times. You may have a fine coating of beer stone that you can not see and this will take it off. I passivate a bit more than that, but I brew a lot.