I always get a plastic box out on service day. Any tools I use get chucked in the box. You then put all the tools away except for the ones in the box, have a look round for any bits you didn't disturb but might need to (mudguards typically for some reason no doubt related to domed nuts), then chuck out the duplicates and hey presto, one bike tool kit.
I hate "what if" stuff and have repeatedly threatened to chuck stuff I havn't used off the ferry, but some bits I think are just useful. I carry a cap type spark plug tester because I've seen plugs that'd spark near the edge of the hole but not in it (*****y Triumphs!) and a multi socket (lots of little pins) because I've used them to shift rounded nuts before. Did you get Chris Scott's book? His list is a good start.
Where you keeping tools? Bits of drain pipe on the sump or rack are popular, but I'm betting every thieving scrote between here and Timbucktoo knows that but can't get your seat off or be bothered to open a pannier.
Andy