I don't usually count my runs, but when I do that:
I first do ~25 runs and check how much time it takes. Then I calculate the average time per run. After that I just put timer on and start doing runs as long as I want to. When I stop, I check the time consumed and divide it by the average time per run to get the amount of runs.
It's not 100% accurate, but very easy way to do this. I have used the pen & paper method but often I forget to mark the ticks because I concentrate on playing the game...