Using reeeeach!
I'm not certain that this is fully allowable - and if it is not, someone please let me know!
One way I've made good defensive use of a reach weapon is by reading a partial action - attack, then 5' step.
As you can ready a step as part of a partial action, your reach-wielder can stay in place, and reserve an attack against a foe who moves into the 10' threatened space.
Your action is triggered, and you make an attack normally, then take a 5' step away from the foe. Your initiative now falls just before theirs in combat.
If the foe still has movement left, they can take it to approach you, but many enemies don't think to hold some movement in reserve. If you step away to the side of a charging foe, for example, they can't deviate from the straight line path.
On the matter of attacking over friendlies into melee. I don't have the handbook in front of me, but I am almost certain that a friend in combat with a foe gives a 50% cover bonus to the foe. That provides the +4 to AC. If you hit the cover (miss within that 4 AC point spread), it does no damage, because the pointy bit of your reach weapon is not in the cover's space. Your friend just gets jostled by the haft of your polearm.
Edit to add; Additionally, I would have liked to see an option for 'pressing' a foe - forcing them back or away. My thought on it is as follows:
If you can assault an opponent with a fearsome and withering attack, but still provide them the opportunity to move away, it can be possible to force your opponent to move. Pressing a foe can be useful for coralling enemies together for capture, forcing escapees back into cells, or dislodging defenders from cover.
To press a foe, you must first declare that you are pressing, rather than attacking for damage. You indicate where you hope they will move, then make a single attack against the opponent. If the attack succeeds, you and the foe being pressed make opposed checks (your Bluff or Intimidate versus the foe's Sense Motive).
If the foe suceeds, he may choose to stand firm, accepting the damage, or move 5' away in any direction to avoid the attack. If the foe fails at the Sense Motive check, he moves to the space you indicated as the target space and takes no damage.
=M