Electrical/Lighting
Battery: The battery may be difficult to examine physically. If the bike turns over easily you can assume it's in half-decent condition.
Kill Switch: Flick it and see what happens.
Kickstand Safety Switch: Make sure the engine dies if the bike is placed in gear with the stand down.
Clutch/Neutral Interlock Switch (if present): Ditto.
Wiring Harness: Look for any signs of obvious damage. Unless you pull half the bike apart it's impossible to fully examine the wiring harness, but at least check the area around the steering head and under the seat and shine your flashlight under the tank. A big cloud of smoke and a shower of sparks when you turn the key is always a bad thing.
Charging System: If there's no charge indicator, start the bike and let it idle; turn on the high-beam, a turn signal and a brake light. When you rev the engine the headlight should brighten. This isn't a very accurate test, but it will give you an indication as to whether or not the charging system is working.
Headlights: Check high/low-beam and indicator (flasher if so equipped).
Check that each of these is functioning:
Front And Rear Brake Lights
Turn Signals And Indicator (and self-canceling feature if it's there)
Indicator And Instrument Lights
Road Test
Some things just can't be checked when the bike is stationary. I recently looked at a very nice motorcycle that passed every point on the checklist. The only problem was that it jumped out of third gear. It's a serious issue and one I wouldn't have found if I hadn't ridden the bike. When I mentioned it to the seller he just smiled and said, "Oh, yeah, it's been doing that." The problem is that in this day and age a road test might not be that easy to come by. If it comes to a test ride I'd suggest asking very nicely and offering up enough of a deposit to show you're serious. At the very least the seller should be willing to run you around the block a time or two. If the owner consents to a road test, remember you're on someone else's bike-you can find out all you need to know without riding it like you stole it.
Clutch: The clutch should engage smoothly and shouldn't slip.
Transmission: Although every bike has its own idiosyncrasies, in the main the tranny shouldn't whine or howl, it should shift positively and under no circumstances should it jump out of gear.
Tracking: The bike should go straight with only light handlebar pressure.
Handling: This is largely subjective, but as a rule of thumb if you're not happy with it now, chances are good you'll be miserable later on.
Engine Performance: Intrusive vibration, odd noises under load and a lack of performance are all cause for concern. In short, the engine should run sweetly, pull with authority and sound like it's in good shape.
Grin Factor: A bike can pass all the other tests with flying colors. But if it doesn't make you smile when you ride it, pass. Somewhere out there is a bike that'll make you grin like a Cheshire cat every time you ride it, and half the fun is searching for it.
What To Take
Cash: You'll need at least enough to give the seller a deposit.
Small Flashlight: Handy for peering into the dark recesses.
Knowledgeable Friend: If he's not so knowledgeable bring him anyway; a little moral support or a cool head is always handy.
Price Guide: Though not a strict necessity, knowing the market value of the bike you're looking at always comes in handy. If you can't find what you need at your local Barnes & Noble, try Googling ("used bike prices" works), ask your local dealership what Blue Book for the thing is, or go to kbb.com.
Notebook And Pen: For the obvious reasons.