Clad gets sorted into pennies, and dimes/nickles/quarters/halves. This is for tumbling purposes, so that when I'm ready to tumble my clad, all I have to do is dump the coins out of the container into the barrel.
Wheat's get a soaking in warm hydrogen peroxide, brushed with a brass-bristled brush, dried, then dropped into a gallon-sized glass jar. Although I haven't found a key-date Wheat, yet, if I did, it would go up on a shadow box on the wall with the rest of this year's keepers.
IH pennies, War Nickels, all other older nickels, and silver coins, go up onto a shadow box for display in my bedroom. There are several areas that coins go to, one for pennies, one for nickels, one for dimes, one for quarters, and one for halves. Currently, this year, I only have four coins on it, a War Nickel, a Merc, a Roosie, and a Washington quarter.
At the end of the year, like most everyone else on these forums that has a digital camera, I take a series of pictures that groups everything together that I found that year. After that, the real fun starts.
I keep my "keeper coins" in two stashes. First, is my "primary" coin collection. It's a binder, with plastic "pages" that hold the 2 x 2" coin protectors. I keep the coins organized by denomination, and by year, starting with the smallest denomination, then on the page, starting with the lowest date, and then by mint mark.
When I find a coin that I already have one of that date, then I will look at both (or all, sometimes I find 3 - 4 coins of the same year/mint) and decide which coin is in better condition. That coin will go into the "primary" collection (or stay there, if it's already in there). For example, say I have a '36D Mercury dime in the "primary" collection, but it's rather worn. It's the only coin of that date and mint in all my coins. Then, sometime this year, hypothetically, I find a mint-condition '36D. It will go onto the shadow box for display this year, and at year's end, will get photographed with everything else, then will be put into a coin protector, and will replace the '36D worn Merc in the "primary" collection.
All coins that do not make it into my "primary" collection go into my "Secondary" collection. This is two gallon-sized glass jars. The aforementioned jar of Wheat's is one of those. I keep all Wheat's, and "secondary" IH pennies in that jar. The other jar has "secondary" Buffalo nickels, and all "secondary" silver.
It's complicated, and involved. But, it gives me something to do on New Year's day, when I'm usually off from work, and can't get out and hunt for long due to weather. However, the past four years, I've been up in Michigan, and still made it out for a hunt on the first day of the new year, even though I freeze my kiester off. I usually scored a Wheat, or other older coin in the process.