Well most bikes have 2 locations for water bottles, I keep either a small pump on the vertical location, or sometimes a little CO2 canister and gage in the saddle bag.
But in the saddle bag I also carry a tire lever, a new tube, and when I'm on my bike (otherwise in my pocket) my keyring with my bike lock key, my skewer wrench, a 4mm and a 5mm Allen Key.
I guess on the off chance someone steals my saddle bag when my bike is locked up I've got no means to change my tire, but it has not happened even in "worse" parts of the city of Toronto. And my keyring stays with me so its not like they have access to the skewer key or bike lock key when I'm off my bike.
Actually for that matter I got a flat on Thursday and I had to replace my rear tube. So I'm glad I keep a kit with me at all times even if its a little bulky. But if you forgo the air pump, it can all fit nicely in a medium saddle bag with room to spare for your cellphone.
Jim