I'm wondering what would be good things to add to resin to make it tougher. Something like JB Weld, but using my existing bisphenol based epoxy, bought in bulk?

You sort of have to keep in mind that different epoxies will have different base properties, it isn't necessarily possible to modify any old epoxy and make it perform like a toughened structural adhesive. If your application is structural, use a proper structural adhesive.

That said, it is certainly possible to make a really strong general purpose adhesive for non-structural applications. Cotton flock is a great additive for this, and you can add fumed silica to make it more thixotropic. Generally those two on their own will make a pretty good adhesive. Talc or calcium carbonate are also good bulkers that increase the density of the resin and make it a bit tougher. Then if you need to do other things like make the resin stiffer, you can add milled glass/carbon fibre. There are loads of additives you can use, this thread could go on forever. But cotton flock and fumed silica are the two that I would use. 

Just remember that some additives will influence the colour quite a lot.  eg fumed silica in any quantity turns the mix opaque white.  Milled carbon turns it charcoal black.  Glass in larger quantities will turn it a bit of a semi-translucent murky grey colour. 

Warren Penalver
Easy Composites / Carbon Mods - Technical Support Assistant