if your standing next to and ally that has a enemy in front of him there is no penalty due to cover. Would there be some effect of cover if you are behind your friend and using a reach weapon?
Actual wording from the rules would help.
To determine whether your target has cover from your ranged attack, choose a corner of your square. If any line from this corner to any corner of the target's square passes through a square or border that blocks line of effect or provides cover, or through a square occupied by a creature, the target has cover (+4 to AC)...
...When making a melee attack against a target that isn't adjacent to you (such as with a reach weapon), use the rules for determining cover from ranged attacks...
...Soft Cover: Creatures, even your enemies, can provide you with cover against ranged attacks, giving you a +4 bonus to AC.
Emphasis mine. Yes, attacking with a reach weapon through a square occupied by a creature than can provide cover vs. a ranged attack will do the same for the reach attack.