Maybe I'm just a terrible digital pet owner, but there's always puddles of pee and destroyed furniture around because I never catch the pets in the act, and therefore I can never make a sim scold the bad behaviour.
Is there a mod out there that makes scolding bad behaviour (peeing inside, destroying furniture, being hostile, etc.) autonomous for sims? Or praising good behaviour (eating pet foot, using the litterbox, staying off furniture, etc.)?

Probably wouldn't work because not everyone has the same idea of what good behaviour is. e.g. I like pets on the furniture and some people like aggressive pets that chase the neighbours.

True, but I could go for one that's just scolding destruction/scratching & peeing indoors. That seems like a universal want.

Something that I find helps with furniture destruction (although I suppose it could be considered a little cheaty) is boolprop controlpets on. Then you can make the dog/cat use their chew toy/scratching post and have the sim waiting nearby to praise them. They tend to get the idea after a few goes at that. As for peeing, a litterbox makes you not need to worry with cats. Dogs unfortunately will still make you do it the hard way.

I appreciate the tips, but that's not really what I'm looking for.

You won't find what you are looking for because there is no coding for a sim to notice what a pet is doing and have a reaction to it. There has to be something a modder can work with to be able to make a mod.

There is cheat object ingame or you can just download this: http://www.modthesims.info/download.php?t=197813
You can set their behaviors as you like and forget about scolding-praising.