Inductor together with all of the decoupling capacitors on the analog side forms an LC low-pass filter, which reduces the noise from the digital circuit. So, figure out the highest frequency of the noise that you want to reduce and calcualte the inductor value as for an LC filter. Or you could just pick the biggest inductor value that would fit your current rating, mechanical constraints and budget.
Another approach in addition to inductors is to use separate voltage regulators fro digital and analog. It's highly advisable to power the analog circuit from the linear regulator.
Yet another approach is to use ferrite beads instead of inductors. They work well at high frequencies (from tens of MHz to hundreds of MHz).
Also make sure that analog and digital and power circuits are star-grounded.
P.S. By the way, what kind of instrument are you building?