I like using a wear-under-your-clothes security travel security pouch for most of my tools. Has multiple pockets and zippers for organization. Also holds keys, MNR/LIRR bike permit, emergency $20 bill, quick links in a few different gauges for emergency chain repair, extra presta valve stem nuts, etc. Sometimes I'll throw in credit cards, though lately I prefer a Lezyne Caddy Sack for real wallet-ey things. If I'm riding with luggage, the pouch gets thrown into my pannier. If I'm riding light, I can put it in a jersey pocket and string the shoulder strap cross body over the opposite shoulder. Very easy to bring from bike to bike.
I don't generally keep a tube in there, mostly because the different bikes I ride use different (in some cases radically different) tube sizes. For tubes I use small or extra-small underseat bags that can stay on the bike they go with.