I used to do that, then I realized I would rather have spare parts just sitting around. Most people with spare bikes swap parts, something about the comfort of the A bike.
Seriously I do both. I usually carry the following....
Fairing stay
Clip-ons
Rearset parts
second set of wheels, extra carrier
Clutch (full clutch with pack)
Full assortment of various hardware (nuts, bolts, washers, gaskets, gasket maker, zip ties)
For anything more than that, I'd move to my spare bike.
Also, the spare bike has been helpful for friends that ball up their bike so that they don't waste a 20 hour round trip and not get to ride.
For tools, I'm the WRONG guy to ask. I take a full height roll-on tool box, filled with both metric and SAE regular and stubby gear wrenches, combination wrenches, full complete sets of 1/4, 3/8 and 1/2 short and tall metric and SAE sockets (including the 32/34/36mm ones for axles, steering head nuts, etc), screw drivers, allen wrenches, all kinds of pliers, safety wire/pliers, bike specific tools, 3/8 and 1/2 torque wrenches. That roll-on is purely for my race trailer. Also, a pancake compressor, and bike specific tools. Milwaulkee cordless impact wrench, cordless drills, feeler gauges, crescent wrenches - heck just about everything you'd need to do anything less than an engine rebuild. I decided long ago that for track weekends (car or bike) I'm better off having a complete trailer set rather than trying to move stuff from my shop to my trailer and back all the time. I'm a tool junky.