Match the altitude!
A bit left-field, but if you're on an Airbus with the capability, load a time marker with the desired time and start descent when the FMS tells you to.
On the Flt Plan page of the FMS, keep an eye on the altitude at the time marker and the altitude at the required position. Adjust the speed as required to match the altitudes and, voila, you'll be there within a second or two. Assuming you're on descent, if you're higher at the time marker you'll be late at the position and vice versa. (It also assumes you have some brain space left at the end of a long sector!)
I'm sure not all aircraft have this capability, but if yours does, try it.