This drives me nuts; it takes quite some time to spin thin singles, and I don't want to waste any!
So here's what I do.
Get yourself a small, accurate diet scale (costs about $25) and weigh your empty bobbins (with leaders on) and write the weight on them, thusly:
[weighing empty bobbin; note weight written on it]
Then, spin your roving. All of it. Don't worry about how full the bobbin is, just fill 'er up. When it's full, start on a new (previously weighed) bobbin.
When you're finished spinning, weigh your now-full bobbins. Subtract each one's "empty weight" and you'll know how much yarn is on it.
Total that up, and divide by the number of plies you're planning (example: 4 if you're making 4-ply yarn). This is how much (by weight) should be distributed to each bobbin. Now comes the tricksy part: rewinding.
I use a hand-drill with a chopstick in the drill bit as a rewinding tool. Pop on an empty (weighed) bobbin, and wind on singles, weighing the filling bobbin periodically to make sure you get the right amount of singles onto it. Repeat for each plying bobbin. With an accurate scale, you should be able to get the same amount of yardage on each bobbin to within a few meters! One other advantage to rewinding bobbins is that you get much more even plying - the rewinding ensures more even unwinding and helps to control "pigtails".
I've managed to reduce my waste to a few meters at most. Woohoo!