Any thing which will neutralise the smell, maybe bicarbonate of soda. Don't use disinfectants as that can make the smell change but you need a neutraliser brushing it in to the floorboards. Does your flooring go all the way under the toilet or is it cut around the toilet?
Could also be old urine around the seals of the lid, if it is only when you lift the lid then it probably isn't the floor. If you have boys then they can spray a lot of wee around and this can get under the screws etc that hold the lid on. I would take the lid off, scrub and soak the whole lot in the bath, scrub the loo where the seat was and then replace. If you have a wooden seat it may just be the seat itself needs replacing.
The floorboards are cut away around the loo. I'll try taking off the lid entirely and scrubbing that first, then if that doesn't work I'll go for the floorboards! It's a plastic loo seat so I don't think the wee is ingrained in it but it could be in the hinges-I hadn't thought of that.
I don't have sons yet (pregnant with a little wee sprayer at the moment!) but I do have a DH who has been known to not bother turning the light on in there at night...to be fair to him, he usually sits down if it's dark though!