Khornette's post and the guide are both very accurate and informative.
Just to add some information; we have found after doing about half a dozen of tier 3 faction leves that certain runes have higher affinities of dropping from specific faction leve pathways.
The following is a list of runes (listed as their respective equipment) we have gotten from the tier 3 special missions:
Bloody Scales - Buccaneer's boots, Buccaneer's sash, Harl. Cap
Tarbh Uisge - Buccaneer's shirt, Templar Hauby, Harl. Acton
Wolfsbane - no rune drops yet
Edit: It would be nice if we could eventually compile a more detailed list of rune drops from other people's experiences since there isn't much info out there regarding this yet.
Edited, Mar 11th 2011 11:16am by lightacadi
Basically its this^^
Tarbh Uisge drops all Runestones for Body pieces + random belt pieces.
Bloody Scales drops all Runestonss for Head pieces + random belt pieces.
Wolfsbane drops all Runestones for Leg/feet pieces(not enough confirmed information on this) + random belt pieces.
We have never seen a head or leg/feet piece drop from Tarb, while we never saw a body piece drop from Bloody Scales or Wolfsbane and according to all the people I know from other shells on our servers who did Leve NMs, it was the same for them. Edited, Mar 11th 2011 10:12pm by Shezard