Heya! I mentioned D20 "Weird Wars" in another thread a few days back, but I'll bring it up here as well; there's one particular mechanic that may help you get that "assassination" feel.
In the WW system, a character which at the mercy* of another has two options; they can surrender, or they could make a break for it and try to bring up their weapon, or run, or perform any other action.
If the latter is the case, the two parties roll initiative, with the first character (the one who had the other at his/her mercy) gaining a +5 circumstance bonus to the roll. If they beat the other player, they get to take a Coup de Grace action. If they roll lower than the defending player, they still get to make an immediate attack, rolling to hit normally.
*Meaning, the character is Surprised and does not have a weapon at the ready.
If it were up to me, I'd probably tweak the above mechanics a bit; saying that the Assassin could attempt a Coup de Grace on an unaware target, but both individuals would make an initiative roll as in the example. A higher result on the Assassin's part means that he could make his Coup de Grace as normal; a lower result would mean he makes an attack roll against his (flat-footed) opponent normally. If that attack roll hits, the damage is automatically considered a critical hit (which may kill the target outright, anyway).