Fresh chilies can be frozen. Just rinse them and keep them in a container or plastic bag in the freezer. Most of them will collapse a bit (some of them a lot) upon defrosting, and will therefore not be suitable for recipes where slices or strips of fresh chili is required, but the flavour remains the same, and they are therefore eminently suited for cooking.
I had some left in the freezer from some plants I had bought in a store last summer (and some ginger that needed to be used), and made this quick sambal oelek-type sauce:
(All measurements are approximate and to taste)
200 g whole chilies, your favourite kind or mixed, defrosted or fresh
2 whole heads of garlic, peeled
2 large knobs of ginger, peeled and chopped
1 stalk lemon grass (also from the freezer)
1 dl white vinegar
1 dl olive oil
1 tsp palm sugar
Blend all these ingredients, heat in a pan and simmer for about five minutes.
Then add 1 tsp salt or to taste, and the very finely grated zest of an organically grown, or at least unwaxed/untreated lemon.
Let cool and keep in a sterilised container.