There are numerous ways to mark snakes for pop counts, none of which are what I would consider 'non-invasive'. Pit tagging, etc gets expensive and is hard to do unless you've been trained in it, scale clipping is only reliable short term and wounds the snake, dyes, etc are VERY unreliable due to the shed factor (and the visibility issue, exposing the snake to predators, etc).

Ironically, photo ID CAN be used quite successfully long term with certain species (some kings/garters/natrix) if you use a part of the body that is definitive (ie not the whole snake). If you are REALLY interested, pm me with your locale and I can probably give you an idea of what has worked in your area in the past. It also depends on what you would really need the data for.

Hope it helps.

Cheers,
Kat