My current practice is to have a side-bound 3X5 spiral notebook for each plane. In the beginning of the book I note completion date, intial equipment configuration (radio, motor, gearing, prop choice, etc.) and weights. Then for each session I note the date and the site. For each flight the flight number for the airplane, the battery I used and the flight time, followed by any notes that seem relevant at the time on how it flew, new maneuvers or other accomplishments, unusual events (including crashes). Configuration changes are noted in the book when they occur (trying new props, CG shifts, receiver/servo/speed control changes, that sort of thing).
I'll also note at each session some idea about the weather - keeping a copy of the Beaufort scale to refer to is a great idea since I seldom actually have my wind meter with me.
In general each battery cycle is a "flight" no matter how many touch and goes I shot. The only exceptions are if there's more than a few minutes between one landing and another takeoff. Then even if it's completing a discharge cycle, I call it another flight. I find this happening more and more with lithiums...... Sometimes I just can't stand to fly the whole thing out at one time.
Lately I've also started noting, from the back of the book forward, any static test numbers on power systems for/in that plane (RPM, current, voltage, power, prop, battery, motor, gearbox), rather than keeping that sort of thing in a separate book. It's easier to find that way in my messy workroom.
I sometimes also go through and add up times on motors or cycles on batteries (they each get a unique identifier, though not as well thought out as Mitch's system - more like "Kokam 1020X2 #1" or "300 NiMHX8 #3" or "P3000X10 #4") just for curiousity or to see how long it took a can brushed motor to wear out.
It might be fun to put this info into a computer, but I'm not sure I could stand to re-enter it all. Access, my goodness that's a major heavy duty tool for such a thing, no?