From what I have read/been told is that it doesn't matter on Lithium ION batteries. Old batteries it did but newer style batteries don't have a charge history or anything of that sort.
Its supposed to 'condition' them so you more accurate battery readings and supposed life; but as Lakers said ^ there really isnt a need with newer LiON batteries.
I did this once after I installed a launcher since I felt the battery bar wasn't accurate. But it didn't do anything.
On laptops, some manuals say to discharge it fully and charge it back up to calibrate the battery every few months or so.
I believe Android Central put up a post once pointing to a post on Google+ from someone at Android saying battery conditioning and those apps that wipe bat stats aren't doing much of anything because once you plug your charger in the stats counter resets itself anyway.
Does nothing.
There is no memory effect *AND* the smarts in the battery can compute how many full cycles (full cycle is the amount of energy from empty to full) the battery has been through, even with partial charges.
I'm getting the Mugen 4600mAh extended battery; would it be better to "condition" it per the instructions, or not??? I'm happy to just use it, if it doesn't make any difference; but it is expensive, so don't want to mess it up. :-$