Fin clipping is used to determine batches of fish, or a single fish in a pond. Unless you clip a different fin off of a fish, there's no way that I can tell 2 fin clipped fish apart a year later if the fins are clipped in the same place.
I use a scissors and will cut off the adipose fin on catfish, or one of the pelvic fins on spiny fish.
I've heard of a hole punch being used to punch a hole in a fin, or part of another fin "trimmed". But, fins will heal back up, and it's hard to determine quickly if it was trimmed or not. Sometimes the rays in the fin are a bit squiggly where it grew back.
Tagging has it's advantages and disadvantages too. Metal tags on the gill plate, numbered and non-numbered floy tags or PIT tags. Gill plate metal tags, and floy tags can be numbered and you can track individual fish, providing the tag stays in the fish. Anywhere the skin is broken on the fish leads to a possible infection site. PIT tags are expensive, but I think the best way to tag fish. Do I think it's a viable way for a pond owner to tag fish? No, I don't think most pond owners will outlay that kind of money.
http://www.psmfc.org/program/pit-tag-information-systems-ptagis I haven't seen any prices on the tag readers, but I have seen prices of $5/tag for the PIT tags.
