It's difficult to do, but I reckon it's more fun to kill them and then kill all the guards and get away in an impressive fashion anyway. Then you hear them shout "Where'd he go?!" And all the women screaming. >.>
That would be a Ninja Assassination... assassinations in general don't have to be secretive, just unexpected... but in relation to the game, from memory I don't believe I've killed a target without anyone knowing..
With the exception of roof guards, I hardly ever kill people without someone noticing! But heh it's more fun when you have to run across the rooftops to get away and find a haystack to hide in. I also like killing everyone then dropping their bodies down a well :')
I've managed it once in the first game, it was near the end with the guy on the boat and it's still one of my proudest gaming moments
The later games have made it a lot harder, I feel that there's a lot less freedom in how you take them out. That's not always a bad thing mind, I like it when it gets a little crazy and you're left standing off against 15 guards
Managed it a couple of times in AC1, truth be told though I don't like stealth and have always been more of a go in murder everything kind of guy so I rarely use stealth unless the game will desynch me if I'm detected which is incredibly annoying.