As I say every time I post, none of this is easy - and many of these rules would strike out decent breeders, but better to rule out a few good ones when avoiding the bad ones.
There will be other stuff too. A degree of gut instinct for sure.
As a minimum, I would want:
Pups that look happy and relaxed in the home environment
Pups that are happy and excited to see people, not hiding/nervous
Pups that are interacting with their mum - worth pointing out that mum will often look a bit scraggy at the time pups leave, major post-puppy moult is entirely natural
Healthy looking puppies - bouncing, bright eyed, clean coats, happy - clean pups and surroundings, not a smelly environment
Proper records of worming (and official documentation for vaccination if relevant)
Evidence of health testing for both parents in the form of KC/BVA results sheets or DNA test letters - often you will just see this for the father, 'better value' to do this for the one dog that you can then use on multiple bitches! Note that 'health checked' is not the same thing as health tested ...
Both adult dogs and puppies to be obviously comfortable with their owners.
I would avoid:
Shy litters - there can often be one quieter pup, but as a whole the litter should give the appearance of being well socialised
Anyone advertising multiple breeds (and even worse, multiple crossbreeds)
No dirty eyes, bums, extended bellies
Any sob stories about lonely last pups, or 'has xx health issue, but all will be fine' - this should be the breeder's issue, not yours.
For any licensed breeder, I would Google them (including postcode and puppies, rather than just name) and I would contact the local council to see how many dogs/breeding bitches they are licensed for.
No breeder should ever ask you for a deposit before they have met you and grilled you on your circumstances, shown you evidence of adult health testing, and not before they know they have a pup of a viable age.
Most of all, do not ever go and visit a pup, be shocked at its environment and condition and pay the scum that have caused it. You may 'save' that one pup, but really what you are doing is rewarding the breeder and consigning the adult dogs and further puppies to the same. Far better to walk away and report to the RSPCA/Trading Standards.