I'd say you have to look at why flanking is beneficial if you want to go down this path: flanking works simply because a combatant's feels threatened from both sides, and his attention is divided between foes on either side, so he can't raise a defense as well against both.
Now, we all know that, but taking that into account in the context used here, I'd say that only conjurations that are actively threatening the target could possibly be used for flanking purposes.
If the conjuration is like one the cleric conjurations that doesn't attack normally (even if they do attack conditionally), or Mage Hand as Liebot mentions, then I'd say no. If you're not worried about getting hit from behind by one most of the time, you're not penalized for being "flanked" by it.
If the conjuration in question provides an active, ongoing threat of attack or damage and pain... I could see someone making an argument for it being distracting enough to give a flanking bonus. I'm not saying I'd allow it personally, but I could see someone making an argument to do so.