My boyfriend's mum never does any housework, and staying there makes me very uncomfortable. She's going away for a weekend, and my boyfriend and I agreed to stay at her house to look after her dogs. Would it be wrong of me to clean her house?

Good chance you could open a huge can of worms here as if she doesn't want it clean and you do it, she could take it as an insult that youre accusing her of keeping a dirty house, which would be true.  While it would be a nice gesture, its a catch-22 situation as to how she will react as on the other hand she could appreciate it but personally I think you need to ask your BF what he thinks

I wouldn't do anything major.  It might be seen as an invasion of her privacy as well as insulting.

I would definitely clean her house!  Maybe she just needs some motivation.  If you work hard on cleaning her house, she will be guilt into keeping it clean (unless she has no morals!).