Not a tool pouch as such, but I have made pouches to store each individual tool within my saddlebag to stop them making a racket.
I don't store an actual spoke, but I do carry a fibrefix spoke as an emergency. The inner tubes are stored in their own pouch's too so holes don't get rubbed in them.
Also within the saddlebag is...
The pump.
Puncture kit inc levers.
Crank bros multitool.
Easy link chain tool and spare links.
NBT2 tool (cassette lockring remover)
First aid kit and emergency blanket.
Rain cape.
Spare gloves.
Jelly babies.
Sometimes a flask of hot tea for those cold days.
Snacks for longer rides.