In reply to Trangia:
+1 for zaflora
another option which I use for my rather minging trail shoes is to pop them in the machine on a short 30 degree wash with Halo Sportwash (picked it up from Sainsbury's).
Not sure how antibacterial it really is, but its a great detergent for running kit, and does a great job on the inner soles, and the whole shoe if you clean them in the machine.
Storing them when fully dried with a tumble drier sheet tucked in them seems to do the trick for me.