I especially liked the twist - that Sim was not going to recover from the surgery and live out his 5 days...
Me, too. I see the setup differently than a lot of folks...there is no initial plan by Phlox and Archer to "kill" or "murder" Sim, but to let him live out his full lifespan (of 2 weeks). When we see Phlox caring for the child, nurturing him, educating him, letting him take apart medical equipment
...I came away with the impression that Sim's surrogate father would give him the best life possible. And it was poignant for me to see Archer spending time with young Sim, but having such mixed feelings about getting close to him, with the possibility of losing Trip already weighing heavily. Archer's physical deterioration over the course of the episode was a very effective way, IMHO, of showing how his decisions regarding Sim were tearing him apart.
I agree with you,
bluedana,, that the discovery that Sim won't survive the surgery is a terrific example of Trek's "no-win situation" scenario. We know at this point that someone will die. What made it bearable for me was Sim's nobility toward the end...his decision not to escape the ship, but to stay and save Trip, for the sake of Lizzie and the rest who were lost. The scene between Sim and Archer in the launch bay, as Sim takes the burden off Archer's shoulders, was very touching.
I agree that Similitude was one of the strongest morality plays featured on ENT, and that, coupled with Connor Trinneer's superb performance as his clone, combined to make for a superior episode. It is right up there with my favorites.
It gave Phlox the opportunity to give of a glimpse of his parental side (we know he's the parent of a number of children.) It's obvious Phlox genuinely cared for this young boy by the way he nurturing him into adulthood. I can only imagine how difficult it must've been to invest so much of himself in Sim, knowing that he would only live for 2 weeks.
Watching Archer's emotional turmoil, eventually manifesting itself physically, seeing this bright young boy, wise beyond his years and with more than a touch of Trip, grow into a man that would have to die in 2 weeks, was heart wrenching (heck, Sim was a very likable character, and for Season 3, having Archer show range in this direction was refreshing.) It quite obviously tore him up to give the order for Sim to be terminated for Trip, but unquestionably, Trip was #1.
Archer was already dealing with so much to this point in the season, only now coupled with the potential loss of his chief engineer (and friend), that the burden of knowing that should Trip's transplant be unsuccessful, he would lose both his friend, and his friend's clone (by default, in 4-5 (approx) more days.) Very tough to take after everything him and Trip had been through.
Sim's ultimate decision to willinging allow himself to be sacrificed for the sake of Trip, and (agreed, bluedana) take the burden off of Archer, and show really how much of Trip was really inside of him, was strong writing. Archer had made the decision, and would've had to enforce it, but Sim made the self-sacrifice for all involved, knowing it would cost him his remaining days.
Sim carried so much of what made Trip a strong individual and what made him so important to Archer (and the crew) that his ultimate loss was felt initially as much as if it had been Trip who had passed. I know those that interacted with him must've have felt his absence quite profoundly, even if Trip was there to "replace" him.
As an aside, as posited by a previous poster, it would've been an interesting twist if Sim had survived (with Phlox somehow extending his life span) instead of Trip. Not my personal choice, but interesting to think about.
OK, I do see some similar moral issues... BUT please, for the love of Q, don't ever again compare one of the franchises biggest embarrassments (Tuvix, naturally), to one of it's finest moments... It breaks my fragile little ticker. 
