i'd have to say the Unjust War.
the Creation of the Unjust path proved many conspiracy theorists right in their "OMG WUT civil war" stuff, and then the war stemming from that, (ie the Unjust war) showed just how easily allies could flip flop on which side they were on. in my opinion it made alliances search more independantly for a secure spot in the political world by searching out treaties with alliances who they felt secure with. not necassarily because of their friendship but because of their power and ability to fight.(this dosn't apply to all treaties, just seen as a rough overveiw)
The Unjust war changed the way people veiwed MDP's and the way the political players went about creating CB's and how treaties themselves were written and acted upon.
wars before that such as GW2 and 3 were more two sided, in which there was the league vs WUT, or Aegis vs the Coalition because at that point in time, although less evident for GW3, there wasn't as much of a tangle in the MDP web, and alliances couldn't use the "conflicting interestes" excuse as readily as it was used in the previous war.
the Unjust War in my mind set a standard for the dominant side of the MDP web. and thus brought out many more of its enemies within the shadows. breaking up those alliances such as Genmay, GOONS and \m/ also allowed for their former membership to dispurse and join various other alliances whether to bring about more of a "opposition" to the current order, or to stabalize the battered and broken side of the MDP web.
since then the lines have been blured and much harder to distinguish who is gonna be on what side, and what not.