I have a big tub of Simple Solution stain and odour remover as Mary's a nightmare for not using his tray! It's also useful for other household stains, and with a 9 year old and 11 year old staying every other weekend it's been needed a few times for spillages! It works great, you just pour it on the stain, give it a bit of a scrub, mop up the excess and leave the rest to dry out. It does take a little while to dry if you've used a lot but whenever we've used it the stains been completely gone within a day.
Unlike a lot of household cleaners, it also breaks down the ammonia which causes the smell and may cause your bunnies to pee in the same place, so might help prevent future accidents too!