There are no rules for organ pipe tone.  Common wisdom among
pipe makers is as follows:

For flute-like pipes --

  Fat pipes are duller sounding than thin pipes.
  Soft material pipes are duller than pipes made with hard materials.
  Stopped pipes are duller than open pipes.
  High wind pressures produce fewer overtones.
  Low wind pressures produce richer overtones.

Pipes with freins follow the above patterns, somewhat.

Pipes with reeds are not easy to explain without diagrams.  Reed tone
is governed by reed composition and dimensions, as well as the resonant
chamber design before and after the reed.  A small resonant chamber
before the reed is more trumpet-like.  A large chamber before the reed
creates a more hollow sound.

Pipe making has been a craft handed down through the generations with
little useful originality introduced since about 1600 AD.

All or none of the above may be true, depending on your source.

Bill Finch