All peppers can be frozen and the only thing needed is to make sure that, whether seeded and cut or whole, that they be patted dry really well. Since I use jalapeños a lot in my cooking I freeze whole after a wash, pat dry and placement in zip-lock bags and just take out on a need to basis. As long as they are dried well they will not unreasonably stick together because it's the moisture that causes the sticking.
Select crisp, thick-fleshed chilies that are free from blemishes and have a bright color.
Preparing for Freezing:
No special preparation is needed to prepare small chilies, Just wash them, stem them and pat them dry. Chop large chilies into smaller pieces or freeze them whole. Use gloves when handling peppers and be careful not to touch your eyes or skin after handling them until you wash your hands thoroughly.
Best Freezing Method(s):
Wash, drain, pat dry and place in a single layer of hot peppers on a cookie sheet or tray . Freeze until peppers are firm, and then transfer into freezer bags, press out air, label and seal. Leave 1/2 inch headspace.
Freezer containers should be moisture and vapor resistant and should not be prone to cracking or breaking at low temperatures. Containers should provide protection against absorbing flavors or odors and should be easy to label. Suitable packaging for freezing hot peppers includes freezer-grade plastic bags, rigid plastic containers or glass containers and heavy-duty aluminum foil.
Maximum Storage Time:
Hot peppers can be stored in the freezer for up to 10 to 12 months at 0ºF before they start losing their flavor.
Remove hot peppers from freezer as needed and add directly into dishes while cooking.
Tips & Shortcuts:
For the best texture, considering drying hot peppers instead of freezing them. Cut the entire plant off at the base or harvest individual peppers. Wash them, pat them dry and string them together to hang up in a cool, dry place with plenty of air circulation. Once dry, store in airtight containers in the pantry or freeze and use as needed.
Refrigerating Hot Peppers:
Do not wash. Wrap in a paper towel or place in a paper bag. Do not use a plastic bag. Store in the vegetable compartment of the refrigerator for up to 2 weeks.
When freezing hot peppers just wash, remove stems, and place them whole in freezer bags. It makes a lot less work then chopping them all up. I then take out what I need for a dish and they do not lose their hotness.