I usually stuff most of my small parts into my box, it is a Craftsman 3-drawer. I have one of those screwdrivers with the four tips built in, small and large phillips and straight-slot. I also keep plugs, jets, a small assortment of metric nuts and bolts (in a baggie). If I break a lever off near the end, I will keep it in the box in case I break the current one off right at the perch-some lever is better than no lever!
I changed the chain on the YZ before I ever rode it, so I put the stock chain into the Regina box and it now resides in the toolbox, too. I think there are a couple of grips (just in case), a small tube of grip glue, and a small tube of LocTite that you can get at any auto parts store.
For wrenches and such, I have a basic Craftsman set of metric wrenches from 6 (I think) up to about 14mm, I have a basic 3/8 metric ratchet set, including a "step-down" for the smaller sockets. The sockets range from 6-14mm. I also carry a set of metric allen wrenches, the long-handled type that come in the plastic caddy. I don't like the "pocket knife" type sets because they are too short and don't offer enough leverage. And they can bend more easily if you really crank down on them.
Lastly, I have a basic set of pliers, standard and needle-nosed, wire cutters, and channel-locks.
On top of all that, I keep my kTm toolkit with the special plug wrench, T-handle and bottle-opener (for after the ride!) in there as well. kTm's plug wrench keeps you from having to remove the tank to change the plug, and the entire toolkit with an extra plug thrown in easily fits into a backpack hydration system for long treks through the woods. It's saved my butt a time or two.
All that and some basic ingenuity should keep you and any riding buddies out of trouble in most situations!