If you have had a bike fit and you are just trying to replicate that on different bikes that have similar geometry, the way that MD suggests will work well because it will minimize the effect of seat tube angle which changes the knee over pedal and reach significantly.
If you have a willing participant, the best way to measure your joint angle is to do a brief film of you spinning on a trainer and freeze it with your pedal at dead bottom center (DBC), on a mountain bike or a road bike, that is when the crank is in line (at the bottom of the stroke) with the seat tube. It is not the same as true bottom center, that is the 6 O'clock position. Then you can use a compass to measure the knee angle. The knee angle should be 35 to 40 deg off of straight. Note that this is a different measurement than if you do the measurement statically. If you take the measurement by freeze framing while the person is actually pedaling the ankle movement changes the knee angle and makes it a larger degree of flexion. I like this movement better because is maximizes the fit while taking into account habitual ankle movements.
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2007 Look Dura Ace
2010 Custom Tonic cross with discs, SRAM
2012 Moots YBB 2 x 10 Shimano XTR
2014 Soma B-Side SS