* AdaptationDisplacement: Most people who know of ''{{Film/Clonus}}'' these days learned about it from this very movie. [[Recap/MysteryScienceTheater3000S08E11PartsTheClonusHorror Or MST3K]].
* CompleteMonster: [[MadDoctor Dr.]] [[MadScientist Merrick]] is at first [[BitchInSheepsClothing charming and helpful]]. He has the clones under his care dissected alive when he views the need as arising, and lies by telling them they'll be sent to the mysterious "Island," while lying to the clones' original source by claiming the clones are brain dead and are not living, sentient beings. When one clone's original donor is already dead, Merrick spitefully plans to have her harvested anyways, and tries to kill any clone that resists him. Drunk on his own genius and power, Merrick seems to view himself as some sort of [[AGodAmI twisted messiah]].
* CriticalDissonance: Compared to how most of Bay's films go, the critics were merciful to this one, giving it mixed reviews and praising several aspects of it, with the common criticism that it didn't try hard enough to really be great. However, it was a box office bomb and barely made back its budget, if even that.
* CrowningMomentOfFunny: Jordan in the bar. The bartender says "Straight-up" and Jordan [[LiteralMinded looks straight up at the ceiling]].
* SugarWiki/CrowningMusicOfAwesome: The [[http://www.youtube.com/watch?v=_iu-t1n821M music of the same name]], composed by Steve Jablonsky. Listen as the tension and the emotion slowly builds up...and then suddenly ''explodes'' in a shower of pure, saturated epicness. Seriously, how did this music ''not'' get any awards?
* GeniusBonus: Tom Lincoln's comment about how Six Echo was worth all the money he spent on him when discovering that they have the same finger prints can seem a bit CaptainObvious, unless you know that finger prints are not genetically determined. Not even identical twins have the same finger prints.
** Or retina "prints", which Six Echo uses later
* HamAndCheese
* HarsherInHindsight: The scene where Michael Clarke Duncan has his organs harvested for transplant is all the more unsettling in light of the circumstances leading up to the actor's death.
* MoralEventHorizon: Dr. Merrick's actions are harsh and heartless, but could be seen as necessary extremes to contain a volatile situation which is Lincoln and Jordan escaping. Then he [[spoiler:personally kills Jones, and orders the deaths of dozens of clones because their GeneticMemory is starting to develop]]. Even worse, as this won't stop the same problem from happening again, it's likely he'll just go for the same solution when it does.
* {{Narm}}: "THERE'S A DOOR OVER HERE!"
* NightmareFuel: Michael Clarke Duncan being harvested for organs. Doubles as a {{tearjerker}} as you see what is essentially an innocent ManChild, [[PlayingAgainstType played by an actor that is usually the]] ScaryBlackMan, dragged to his death crying "I wanna live!"
** And the probes that crawled onto his eyes.
** The woman who gave birth and smiled at her baby only to be killed seconds after the child is taken from her.
* TheyWastedAPerfectlyGoodPlot: The film sets up what could be an emotionally wrenching decision, namely asking whether it would be worth it for [[spoiler:Jordan to sacrifice her life so as to prevent Sarah Jordan's family from losing a wife and mother]]. Unfortunately this is rendered completely moot by the revelation that [[spoiler:during her accident, Sarah Jordan suffered massive brain injuries from which she had absolutely no hope of recovering]].
** And isn't it convenient [[spoiler: that they avoid any (more) possible moral dilemmas by making the real Tom Lincoln an absolute douchebag, even though as ''The Onion'' pointed out the clones do a whole load of damage and endanger - and possibly END - lots of innocent original people's lives?]]