Hammerite paint works reasonably well. No idea if it the best, just using it because I had some in stock. I don't like the plastic thingies just in case I lose one (more plastic in the sea). I have been trialling cotton ribbon: 300mm length, halved and cowhitched to a link, no problem through the gypsy and biodegradable.
If you have thoughts of re-galvanizing your chain in the future then don't put any paint on it.
It's very expensive to get the paint off, to enable re-galvanizing.
I use leather bootstraps (once used cable ties, but loosing one is lost to the sea).
We use thick, or wide cable ties. They run through the gypsy without issue and are easy to replace;ace as you deploy the chain.
You can use different colours and establish a simple code, ours is written into the hatch/lid of the chain locker. We mark at 10m intervals but have additional marks warning us we are near the bitter end and when the anchor is about to arrive at the bow roller, marked every metre for the first 5 metres (you can also identify howe much chain you have buried , if you are so inclined). Pale cable ties are easier to see in the dark.
Paint wears off, though does stay much longer 'inside' the links - and there is the issue if you want to regalvanise (and I guess cleaning inside the links would be a job for a Grandchild looking for some extra pocket money. If I were to paint, any enamel paint left over from a decoration job and I'd preference red and white (together) - commercial ships use those colours for a reason - they stand out.
Any paint except any that has metal in ... especially such as Lead. I know lead paint is banned - but there are still odd tins laying around in sheds ! Why not ? It corrodes the zinc galvanize.
I use straight enamel paint ... red for the marker ... and white links either side to the number of length.
Cable Ties .... I saw a guy tear his hand open when handling a chain with cable ties. Please think carefully if you are going to use them.
I've been using cables for years, maybe 15 now - no issues. Strangely enough I generally keep my hands away from moving chains - and if the chain is not moving I cannot see how the cable ties would tear your hands. If you are worried simply use the very thin ones as a bunch.
We use any locally available metal paint. Just white at the 10 m points and red at the intervening 5m points. Then coloured cable ties red, yellow and green for identifying 10, 20 and 30m and so on. Leave the cable ties intact so they’re easier to spot and won’t catch your hands should you need to handle the chain.
Using short lengths of coloured webbing sewn through links. Cheap, easy, goes through gypsy with no problems, doesn't catch on anything, won't cut your hands. Been using this system anchoring from UK to Portugal this year with no problems. Checked fully 2 days ago - still in perfect condition.
Also painted links with car spray paint to match but this is all but gone.
I use the smallest cable ties I can and don't cut the tails. greens at 5m intervals, red at 20m intervals, so a red and two greens is 30m
If you want to cut the tails, use a hot knife to melt through, or cut and melt the end a little; that will avoid the sharp edges left by cold cutting and subsequent injuries.
Another cable tie user here. Don't recall losing many but, then again, I rarely have to use the windlass.
As I never do any fancy calculations I put out chain in multiples of 10m up to 45m. This makes matters nice and easy, I put a tie on at 10m, 2 at 20m, and 3 at 30 mts. Above that I just busk it.