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mcfly:
How often or rapidly is the flickering occurring?
Suppose it is often enough that there no problem with you watching and waiting for the occurrence, then connect two 120 V 15 W incandescent lamps in series and bring out three leads. A lead from each end and one from the center of the two lamps. Connect the center point wire to the main panel neutral buss. The other two wires are connected to opposite phases.
You can use higher wattage bulbs, but they are too uncomfortable to watch.
When other lights in the house flicker do either or both of these lights flicker?
If one light brightens and the other dims, then this is associated with current flow on the neutral. If one dims and the other remains constant, then the change is associated with the hot wire circuit from the transformer to the output side of the breaker to which you are connected.
If the flicker at this point is very small compared to the flicker in the house, then the problem probably exists within or on the output side of the main panel. This could include the breaker to the circuit with the flickering lights, or the breaker connection to the main panel buss. This assumes the test lights connected to the main panel are not on a breaker that supplies the flickering lights.
You can do this same test with a DVM or two DVMs, but it is much harder to watch both meters at once or rapidly switching one meter between phases.
Once you have some idea of where to look, then the meter may be the most useful tool to use.
With more information I can provide additional techniques to isolate the cause.
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