I like taking photographs of the thing as I take it apart. However, that's more for when I'm starting with a complete engine, so I know where the brackets go, what goes where, etc..

If you're going to *completely* rework the motor, it doesn't matter too much about parts except the main and rod caps. Since everything would be machined, all you need to worry about are the final tolerances. Obviously you need to measure everything anyway though, and if a complete rework is not your ambition, 440sixpack's tips are good to follow.

I don't like using stamping sets to mark parts, especially rods. Instead I just wipe off the bearing journal with a paper towel, and write the cylinder number on the inside with a sharpie. You could also use the outside, but I figure if it's on the journal on both the rod and cap there's no way for me to mix them up. Also put a little hash mark on one side over the parting line, that way you know how the cap is oriented.

And yes, bag up EVERYTHING and label the bags. I took apart my Cordoba's motor like that, and I know that if I didn't, I'd still be putting it back together. Check the Cordoba link in my sig to see how I did it. It doesn't show the entire bagging process, but you can get an idea of how methodical taking apart an engine should be.