It often depends on what I was last doing.
If i'm training a Pokémon, then I will save in the Pokémon centre close by the location I am training. This is usually in the Resort Area.
The main reason being is that I come back to the centre to heal up after battling, and is often the last thing I do in after a training session before turning off. It's also useful having quick access to the PC to rearrange my party if necessary.
If I am chaining, then I will save in the middle of the grass patch that I am chaining in. This is so that if my chain breaks, I can simply reset so I don't have to buy more Repels after ;-)
But more often than anything, I save in some Pokémon centre nearby wherever I last was.