In PvP, you need to behave like a clone to make them convincing. Using stealth too helps. Another option is to build so that you don't use clones for defensive purposes, but for dot and mass shattering.
In PvE, I found that foes did target my clones often enough, as often as you'd think if the AI was confused and picked randomly. As clones don't last long, I had to supply more to replace those lost.
Well, I said this before, but I found it incredibly easy to figure out which is which in PvP. Granted, the game is new so people haven't perfected it yet and I'm more observant than most, but even if you get tricked by a clone, they have such low HP that you're going to figure it out. Then when you see the dude who makes a new clone, keep him targeted. If he doesn't have stealth, if you just keep him targeted, you're golden.
If you waste an attack with a long cooldown on a clone, then it has served its purpose. Remember that it is pretty easy to make new ones.
Also, I found sometimes that it was a bad idea to only focus on the real mesmer and ignore clones. Unattended clones do add pressure, and they can be shattered on you as well.