With waterfowl seasons just getting under way, it is a great time to think about harvesting waterfowl feathers for fly tying. It is easy to go a little crazy and keep everything but it is really not necessary.
One quick note to be sure you are doing it legally - at least in Wisconsin - I quote, the WDNR regulations, "Sell, purchase or barter, or offer to sell, purchase or barter any migratory game bird or part thereof". So ask friends to save feathers for you but you can't legally pay or trade for those feathers.
Ducks are pretty easy to deal with because largely you are taking feathers off the bird. Any time you are not having to deal with skin, blood, and fat, you have less issues with potential rotting, staining, or having to deal with curing skins. Even with feathers, there is still the potential for mites and other parasites so it it always useful to remove as much "non-feather" material as possible. For feathers, I always do at least a couple of freeze / thaw cycles in the freezer and 15-30 seconds in the microwave just to be safe.
Here is my short list of feathers to consider keeping - in order of what I use most to least:
Cul de Canard / CDC
Flank Feathers
Wing Quills (ducks and geese)
"Shoulder" and Covert feathers
I don't bother with any of the rest - and rarely bother with the wings.
CDC Feathers
Why you should keep them: CDC feathers are by far my favorite wild harvest materials. They have a structure and a natural oil that help them float, making them great for dry flies - like the CDC and Elk, maybe my favorite fly ever. Because of their whispy nature, they are also great for adding movement to nymphs and streamers.
What Species you're Looking for: In my experiences, divers seem to have smaller CDC feathers as do the smaller ducks (teal and Wood Ducks) that are suited for #'s 16 - 20 hooks which you are very unlikely to find in fly shops. If you like the CDC and Elk, divers and smaller dabblers (teal and Wood Ducks) are perfect for this fly. If you don't like the CDC and Elk, we probably can't be friends...
Geese have larger feathers that is better suited to some of the dubbing loop techniques for CDC feathers. They are more like what you find in most fly shops for CDC.
How to harvest CDC feathers: Hans Weilenmann did a much better job describing and demonstrating how to harvest CDC feathers than I can. I take the CDC off of every duck I can, they are my most used wild-harvested feathers or fur.
Links for Using CDC Feathers
Flank Feathers
Why you should keep them: The sides of mature drakes are great for wings on dry flies like many of the Catskill standards, the Henryville Special, and a bunch of others. They also make great wings (backs) for streamers like Galloup's Zoo Cougar, wings for Salmon flies, and hackles on streamers and salmon patterns. Washed, they take dye very well. These are really versatile feathers.
What Species you're Looking for: Each species of duck has a different type of flank feathers. Probably the most prized are those of the drake Wood Duck. Most other puddle ducks have flank feathers worth keeping. Mallard are sort of the standard. No need to go crazy here but harvest off of a teal, Gadwall, Widgeon, and Pintail or two and you should be set for some time.
How to harvest flank feathers: I prefer to take individual feathers and try to avoid the "blood feathers" (those that aren't fully developed yet). Then, I handle them like CDC. Put them in a bag, do at least freeze - thaw - and freeze again cycle. Maybe give them 15 seconds in the microwave if you are still concerned.
Links for Using Flank Feathers
The Hornberg Special
Duck Wings
I'll handle the quills and shoulder and covert feathers in the same section as they can be harvested and handled the same.
Why you should keep them: The wing quills are used for quill wings (duh...) and the inside edge has biots - though they are quite small on ducks. In addition to a number of traditional wet flies, wing quills are used for wings on the pain-in-the-ass No Hackle Dun and some number of caddis dry flies, most famously the Henryville Special. The feathers of the top side of the wings - shoulder through the coverts are useful for wings on some really subtle dry flies like the Rich Osthoff's Duck Shoulder Dun, essentially an easier to tie No Hackle Dun.
What Species you're Looking for: Species matters a lot less here and geese become much more useful, at least for me. You will find biots on geese that are the right sizes for tails and smaller bodies.
How to harvest flank feathers: There are two different ways to harvest these. The most simple way is to harvest just the feathers and deal with them as you would flank and CDC feathers. The other, little more involved way is to cure the entire wing. If you decide to do this, remove all the meat and as much of the fat as you can. Salt or better yet, Borax will help cure them.
On the bird above, the wings, the flank below it, and the CDC feathers on the back end are all well worth keeping but the flank and CDC are, for me, the most useful and easiest to deal with. On Wood Ducks, these are prime feathers for the fly tyer. Dyed Mallard is "fine" but there is no substitute for real Wood Duck flank.
Links for Using Biots, Wing Quills, and Shoulders / Coverts
Words of Warning and How to Avoid Issues
Dealing with wild harvested feathers and fur is not without potential issue. If you, like me, have way too much money invested in fly tying materials, you will want to be very careful and to take precautions when dealing with wild harvested feathers. Some pieces of advice are to deal with them outside or in a garage or shed, do the freeze - thaw cycle a few times, store each harvest in its own zip-close bag. What I mean by that is not every duck's CDC has to go in its own sealed bag but all the harvest from one day should. This way, if there are parasites or other issues, you throw out a lot less material.
Wild game is notorious for having a lot of parasites. Birds are often loaded with mites and fleas. Deer and other furry critters are often full of ticks, mites, and fleas. My best piece of deer hair for "elk hair" caddis wings is loaded with ticks that didn't make it through the tanning process. Typically, most of the parasites will leave the feathers when the animal cools down (this is the #1 reason for dealing with them outside).
The most simple piece of advice is to keep nothing you are not comfortable with. It is not worth it - when it doubt, throw it out. I don't keep anything with blood and do everything I can so that there is no meat or fat and as little skin as possible in the wings before treating them. I go through at least 2 freeze / thaw cycles on all feathers and even the stuff I've treated with salt or Borax gets the freezer treatment. I don't know what the overall risk is but taking every safety precaution you can takes little effort and in 30 years, I've never had an issue but I'm ultra-conservative about what I take and what gets used.