A lot depends on how much
you know about the quality of the fuel you are putting in your tank and burning in your engine. Since the majority of engine related problems seem to come from fuel issues, I triple filter all the fuel (with a BaHa-like water/crud separating filter) I buy and I buy it at a busy truck stop, hoping it will be fresher than fuel that sits for long periods of time at many marinas. My Yanmar diesel also calls for fuel that has a minimum cetane rating of 45. In my area, all of the ULSD fuel outlets I've seen are selling fuel with a cetane rating of 40 so I add a cetane booster. This improves ignition and reduces smoke. All of the fuel polishers I know in this area have long recommended adding the right amount of "Pri-D," a combination stabilizer, injector clearner, and lubricant and so I add a dash of that, too (see link). Short of having your fuel polished (I think you would be better off disposing of old fuel rather than trying to clean it) the best things I think you can do keep your fuel "clean and pure" is to buy the best quality fuel you can find, filter it, and change your primary and secondary filters at recommended intervals.