"Every rogue I have ever played has been built, a la Garrett. Sneaking past or knocking out the guards and generally robbing the bad guy blind before he even knows my character has been there. Who wants to kill people when you can just totally piss of the bad guys? Even better when they dont know you did it!"
This is the classic infiltrator, the guy who uses his noodle to sneak past challenges, take out villains, and make off with the loot before the bad guys even know what hit them. How would you play this guy in practice?
For a start, coshing someone into unconsciousness or otherwise killing them in one hit in d20 is very hard... against anything except low-level mooks, anyway. For a Rogue it's all about maximizing Sneak Attack damage, whether lethal or not... but actually getting up to someone without them noticing you in the first place is extremely hard. Without cover or concealment, a Rogue takes -5 to his Hide check for every 5 feet he crosses in the open; even the lamest guards can therefore probably expect to impose 5 or 10 points of penalty onto your Hide check. If you make it, and the victim remains unaware of you, you can at least forget his Dexterity bonus (whoopidy-do for most armoured guards, but every little helps I suppose) and expect, if you hit, to apply an extra few dice of damage.
Aside from Sneak Attack dice, there's no real bonus to taking someone unaware like this; you'll do no more damage than if you were flanking, or more tellingly, if he actually Spotted you on the way in but you still won Initiative... which for a Rogue is likely to be odds-on. Given the probable difficulty of making that first strike (magic notwithstanding, and one of my players is now a Rogue/Wizard with invisbility and true strike high on his list of spells), it seems to me, unless I'm missing something, that there really isn't that much to be gained from taking someone on like this.
On the contrary, it's likely to be a very bad idea for the Rogue to extend himself from the party and strike at a bad guy without everyone else to back him up (like the party Fighter, who will be hanging back out of range in order to avoid giving the game away). I can understand the balance implications, but it seems to me that a bonus to the Rogue's critical threat range might not be out of order if he manages to get the a strike in while his opponent is unaware (which is of course different than simply being flat-footed). Yes, you don't double the Sneak Attack dice, but it's something... a payoff for taking that additional risk.
With a sap, you can deal non-lethal instead of lethal damage... but there's no inherent rule which makes it easier to render someone unconscious if they're unaware of you. Honestly I would be nervous of any such rule, but its absence renders the cinematic image of the infiltrator quite impossible to play in practice. The Assassin's Death Attack probably comes closest, but it's no coincidence that you have to be at least 5th level, and evil, to use it.