Timbre is the term used to describe the tone colour of a musical note; if two stops of the same pitch and loudness are played, then timbre is what distinguishes them.
The perception of timbre to the listener depends on two things; the attack (start) and release (finish) of the note, and the harmonic structure of the note. The same note played on an organ string pipe and on an organ orchestral oboe may have similar attack and decay, but be differentiated by the harmonic structure.
Organ clarinet stops are usually good imitations of their orchestral counterparts; the harmonic structure (favouring the odd-numbered harmonics) and the attack and release of the note contribute to the success of this deception.