Indexing the spark plug is where you use shims to make sure the open part of the gap faces the intake valve. that way the spark is not "hidden" behind the upper electrode. Makes starting the flame in the cylinder a bit easier.
Note: This is not an attack on the author of this post, just a followup on seemingly everyone's idea of indexing in this thread.
Actually, this is only half true. This is the most commonly taught form of indexing, and in some cases it does work, but in others it does not. Here is why: The engine doesn't care where you point the spark end of the gap because you should be igniting a fuel vapor. The true point of indexing is to face the spark in the direction of the area of the cylinder where the flame will propogate best; the area the charge is going to be most dense in the cylinder just before igniting. Yes, you could face the gap towards the intake valve, where the fuel is coming from, but due to turbulence, the flame may want to propogate in some totally off-the-wall area of the cylinder or rather the charge may build up in some other place. This is where you want to face the spark gap. It could even want to propogate below the plug and not to the side of it, which would make side-gapping a good thing; a FULL side-gap so that the ground electrode is NOT overtop of the hot electrode at all. This is a pretty hard thing to determine, though... I remember a team doing some extensive testing on this, at one point using clover-top pistons, (clover shaped relief in the top of the piston) to try and equalize flame propogation throughout the entire cylinder as best as possible. They had to look for signs on the cylinder walls and piston tops to see where the charge was trying to reside.
In some cases, due to where the plug is in the head, it just won't matter where you face it because it will never get close enough to the charge area of the piston. Oh well. This makes a full side-gap the only possible advantage.
So YES, indexing plugs the commonly-taught way COULD help you, but it would just be by chance that it did because without serious testing, you're never going to know where you need to point them. If you automatically think indexing towards the intake valve is a good idea then side-gapping should also automatically be a good idea because you remove material which could interfere with the fuel charge hitting the spark... unless the backside of the electrode is facing towards the intake-valve in which case you may believe you need to at least turn them side-ways. But then is it worse for the fuel charge to have to split around the electrode before coming around to the spark gap area, or is it better for it to have to hit the spark and then split around the electrode, or should you side-gap and then turn them sideways so that it doesn't have to split around the electrode... this is all IF the intake charge even tries to blow by your plugs. The charge might flow into some totally different route, bypassing the plug altogether. Do you know?
It's probably best to just start with side-gapping since indexing is a whole different animal which takes tons of testing. Worst of all, things like this are influenced mostly by the POWER OF SUGGESTION! It's not that they don't work, it's just that they don't work unless you do them correctly, and in some cases, they cannot make a difference due to head design. But you could SWEAR that throttle response is BETTER and so is mileage... right? Right? Dyno testing is the only real route... or e.t.'s