You can actually freeze leftover canned chipotle peppers in adobo sauce!  Empty the rest of the can into a small freezer bag and allow it to freeze as flat as possible.  When you want to use some, just break off as much as you want and toss the rest back in the freezer for up to 6 months. You could also freeze them individually in ice cube trays, then transfer to a freezer bag once they have frozen completely.