I add headlight and marker light spares and, within reason, spares for whatever gizmo the bike tends to have problems with. On the Bandit that was the vacuum operated fuel valve, on the R6 its a spare fuel pump. Also a compact 1st aid kit and replacement fuses, a few hose-clamps, hex drive drill bits. Agreed wrt the small powered tire pump, patch stuff and wireties. A great idea to add a little multimeter- will do that, and some of those towel things.
When I had the the Bandit, it was set up with larger panniers so I added some additional tools- even a little vise and hacksaw which paradoxically were once very handy on a local outing when I came up on a stranded rider with his chain guard being eaten by the chain.