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So the runes of witnessing increase the odds of getting a psychic power off, but also increase the chance of a perils attack.  If you have a farseer with runes of witnessing, can you choose when to use the effect, or are you forced to always take tests with them?  The description in the codex makes it sound like tests are always taken on 3d6, but it is still just a piece of wargear, so can you opt not to use it in the same manner as you could a special weapon?

I would think because it's not written that you can turn it off or opt not to use it that you have to. I understand why your asking though because both times I have taken them I have periled my own Farseer to death.

How bizarre, in the last game I played against Eldar, only I used the 3 d6, my opponent just rolled normally.  I need to go read that...

Runes of Witnessing cause the Farseer to cast on 3d6 take the lowest two.

Runes of Warding cause enemy psychers to cast on 3d6, any 12+ is Perils.

So the question remains, as wargear, do you have the option of not using them?

The wording of the rule is, "A Farseer with runes of witnessing rolls 3D6..." (Eldar Codex, p. 26).  When wargear/weapon/ability descriptions contain "can" or "may" it would seem that one has the option of not using them.  But in this case, we are not given such a choice.