During The Silence Has Been Broken quest, you encountered Amaund Motierre. As it is soon after revealed he is a man who belongs to the Elder Council. Obviously this is one extremely powerful fellow. If you inquire as to why he wants the current Emperor dead he will make an extremely specific yet utterly vague remark. The information he reveals is in relation to an Emperor from I believe the 3rd Era (it may have been the 2nd). This Emperor (who he names, but I cannot recall the name), was assassinated in order to bring about extremely specific changes to the government. What they are he does not say, however the fact that he mention the year, the age, and the Emperor's name in addition to the reason as to why he was assassinated seems extremely important. And by important I mean foreshadowing. Is any of this really important to the current game? No. From the perspective of someone who loves the lore though? Very important. This little hint of information not only explains two key events, but also lays down the groundwork for some key plot changes. I think that whether or not we kill Motierre is irrelevant the fact that we did kill the Emperor so that Motierre's plans could succeed even without him is important. I honestly wouldn't be surprised in TES: VI if our actions didn't play a huge part in how Tamriel is ruled or runs.
I'd appreciate any help from the other lore buffs out there who might be able to shed some further insight into our actions and just what Motierre was talking about. I apologize if this has been asked/debated before, but I couldn't find any results on it via searching. I figure that eventually I will get around to this part again in another run, that way I can actually record more information on this, but that probably won't be for quite a while.