Pretty little coloured glass bowl (with lid) on the side table. This is what I've seen most people use. Don't be worried about them seeing condom sizes - they won't notice and even if they do it doesn't matter (although the ones that say 'trim' I tend to quickly throw the wrapper into the bin tucked just under the bed )
I leave various sizes out on the bedside table
Mine are in a zipped makeup bag. When it's a large one I'll make a fuss "Oh, you need a king size!" One client said "you probably say that to all the guys" and I said, "no, some of them need super king."