Cut peppers to remove stem and seeds. Put on a fine mesh rack in your smoker at 225 degrees, until dried. Then, remove them and put them into a food processor (or Magic Bullet). Blend until you have pepper flakes, and pour them into spice jars, to spice up any dish with smoked habaneros.

I make this a lot - it keeps in the fridge a long time! http://www.food52.com/recipes/6399_carrot_ginger_stuff

@ChristineB and others about stuffing the habeneros...
If you really wanted to try that you could lightly score the inside of the pepper to open the sacks with the chili oil, then rinse with a high proof vodka or grain alcohol which will dissolve the oil into itself.
Jar them and cover with clean alcohol and leave soak overnight and change again if too hot still.
This should remove enough of the hot capsicasum from them but leave you the flavour. Hopefully it will let you stuff them and cook them without the fruit being too soft from extended pickling. Ive never tried this personally but it sounds like it might work.

I like to lightly pickle spicy peppers with vinegar, garlic, salt, and oregano. After a few weeks., you can use the spicy vinegar on fish or salads. The pickled peppers are greAt on a sandwich.

I also made habañero vodka last year! I didn't bother blending, though. I just dropped three whole peppers into 750 mL of vodka and let it sit for a long, long time (it was at least a month before we even tasted a drop, and we just kept the pepper in there, so it just kept infusing until we finished the bottle in July). WOW! That stuff is seriously spicy! The first time I tried it, I took a big shot at a (quite rowdy) dinner party with friends, and I had to cool off (and stop hyperventilating) on my -5 degree front porch in the middle of Chicago winter. From then on, we used it in awesome bloody mary's (using half habañero vodka, half plain, otherwise it's way too spicy), or to poke fun at my male friends' manliness when they claimed they could take a shot with no ill-effects, only to end up gasping for air or on the floor. Good times :)

Personally, I wouldn't use these babies to make stuffed peppers. Eating a whole habañero pepper would be waaay too intense for a normal human to endure. Unless you have taste buds of steel, I'd choose another option! (Those goat cheese peppers do look delish, though)

I blended a bunch up with vodka to remove the hot oil, left it soak overnight, then strained it.

Now I have a bottle of golden yellow vodka thats like hot sauce. I can cook with it or give as He-Man shots.

Stuff them with goat cheese. This recipe is for elongated chilis, but should work well with different quantities with Habanero. It will be quite spicy though :)

For chilis like in the photo:
250gr fresh goat cheese
2 table spoons grated regiano
50gr chopped walnuts
salt and pepper
a bit of olive oil

Mix cheese, 1 tablespoon of regiano, walnuts and 1 tablespoon of olive oil. Salt and pepper to taste.

Cut the chilis lenghwise and remove the inner white stuff and seeds. Gently stuff with the mixture.

Pad a small baking pan with baking paper and put a bit of olive oil with the finger on it. Lay the chilis open side up and sprinkle with the rest of the regiano. Roast for 15 minutes at 180c in the oven, or until they start to show color.

Source in Hebrew: http://www.mouse.co.il/CM.articles_item,582,209,51612,.aspx

A spicy oil sounds interesting!

I don't know about pickling them though, they are sooo hot. How would I use them?

I did make a great hot sauce which I guess I could freeze. Safely preserving things alway makes me crazy.

(i am onelostshoe)

There's a good basic recipe here for pickled peppers that says it can be used with all types: http://www.foodinjars.com/2010/08/unfancy-pickled-jalapeno-peppers/

Have you thought about putting them in oil? How about roasting them, letting them cool and then marinating in oil -- to make a spicy oil that you can use to finish a dish?