Both has pros and cons.
Not so good cases without filters will suffer on floor being a vacuum cleaner and collecting dust.
On table, you get disturbing noises (good case MUCH less).
Heavy computers on relatively thin desk can cause it to bend.
You can always get/create roughly 10cm high stool that allows you putting computer down even with carpet or so.
As for table, from my personal experience - there is never enough table space.
Plus if it is in a living room, your wife's going to crucify you if you put it on table.
If you go for watercooling with external radiator, it's better to have both radiator and computer in roughly same height, otherwise your pump has a lot more static pressure to handle and overcome.
That's just few points that came on mind immediately. In the end you will have to decide what position is best for you personally.