I also have a spare tire and the factory jack. I have a small box with points, bulbs, starter solenoid, fuses, VR and instrument VR, and a few other small parts. I also throw a small tool bag in there with the basic stuff.
Just a jack, a spare, a tool kit and insurance with tow when nothing else will work. Unless you have an unlimited amount of spare cash laying around, you won't have the right spare part when something goes wrong.
Really depends on the season, right now its soccer gear and we are switching from basket balls to base ball gear. I like to drive it to my kids games - there is nothing like rumbling a cammy set of Flowmasters through a parking lot at my kids outdoor games pretending not to notice... My friends think I was ignored as a child.
Also, battery, quart of oil, pint of power steering fluid, fuses and a Holly gasket set in the glove compartment (never used it in 10 years but its there). Longer trips I carry a spare and accessories. One thing I hate about the battery in the trunk is that its mounted on the passenger side to "offset" the driver which is an illusion at best - I travel on expense accounts if catch get my drift... So I can't bolt the spare down which I hate.
For autocross days, tool bag, pyrometer, air canister, torque wrench - you get the idea - it's a functional area for me.
I have Rags, Motor Oil, ATF and Coolant, and whatever came stock with the car.
I will make a small toolkit bag which will have a cheap multimeter, fuses, wrenches, basic tools (screw drivers) electrical tape and duck tap etc...
Here's an idea for you that probably most people haven't thought of. I've got some Dickies coveralls in the trunk of my daily driver so that if I have to change a flat tire or something, I won't have to risk ruining my clothes.