Canadian semi-soccer-fan here. By that, I mean I watch when it's compelling...generally once every four years. I'm a huge sports fan though, so I tend to look for reasons to watch.
 
Now, as I said, I'm Canadian. What that means is that I have an inherent, built in dislike for any and all things American (even though there's no doubt that the USA is our biggest cultural and political influence...maybe because of that...it's the whole 'elephant in the room' theory), notwithstanding the fact I cheer for a US baseball team, and enjoy my vacations down there, etc, etc,. In any case, let's just say that if the USA is playing some other country in pretty much any sport you care to name, I'm generally cheering for the other side.
 
So, Slovenia 2 - USA 0? Woo-hoo. Down in flames, yanks!
 
Then Donovan scores to make it 2-1. Something about that goal tweaks something deep inside my psyche. Against my rational brain, my gut starts to root for an American comeback. Weird. 2-2...go go go U-S-A!!
 
Then this. A bag-job extraordinaire, as Doc so aptly puts it. And the more you look at pictures and videos (as in the stills above), the more obvious it becomes that something was just not right.
 
Today, against Algeria, I'm solidly rooting for the USA. And to my amazement, there's yet another botched call?! Is there anti-American bias? As one who in the past may have been happy to see it, I can only assume so.
 
In hockey, in basketball, and to a lesser extent in football, and possibly to a lesser extent still in baseball, with the possible exception of the strike zone, we see referees, umpires, officials...make "make-up" calls. Nothing so horribly blatant, but if there's a borderline call that goes one way, you'll often soon after see a borderline call go the other way if there's an opportunity. You can feel it coming oftentimes, especially if it's clear that there's been an actual error that can't be fixed properly at the time the call is made. It's human nature. "Sorry 'bout that lads, we'll get the next one"...
 
Is there an anti-American bias? How can an official (even though it's another official, another day, a different match...in this case the call that came before it was so egregarious that it shouldn't matter) call that offside against the USA, negating yet another goal?? It was close - it could have gone either way - this is true. In most situations, if that call is made, you shrug your shoulders, disagree, and move on resolutely. But, knowing that there was a call that completely messed with their World Cup tournament the game before, how does the USA not get the benefit of the doubt on that offsides call?
 
Is there anti-American bias at the World Cup? My eyes tell me, yep. My heart tells me, yep. And that bias, and the American team's reaction to that bias (little complaining, mostly resolute, overall just a terrific "us against the world" type response), has just earned the American soccer team a most unlikely fan. Because the one thing I'm NOT a fan of, is injustice.

The Jim Joyce call was just as clear in freeze-frame as these images are.  And Jim Joyce thought he made the right call.  He was sure of it.  Until he saw the video.  Then he realized he made a mistake, felt horrible, and apologized profusely. 
A famous experiment was conducted, where viewers were shown a short video of people passing a ball around in a room.  Some of the people are wearing white shirts.  The task of the viewer is to count the number of passees between people with white shirts.  You can see the video here:
Selective Attention Test
The results are pretty astonishing.  IIRC, about half the people who watch this video the first time - including myself - never see the other thing that happens in the video.  You're blind to it, because you're paying attention to something else.
So the Jim Joyce case is completely relevent, and illustrates a real-world case where this can happen.  Joyce a) had motivation to get the call right, b) was as experienced and respected an official as you can find, and c) had a very simple and straightforward call to make.  And he blew it.  The soccer ref didn't have b) and c).  At this point, we can only speculate about a).
 
 
 

One thing I never understand with cries of biased officiating, in any sport.  And that is, if it was biased, why was that call in particular the one that was bent?
Versus Slovenia, why didn't the referee blow the whistle on the other two goals, to keep the Americans from tying it up?  Was it because the ref just couldn't stand the thought of the Americans winning?  Because he apparently could stomach a draw.  Or why didn't he make some random call to give the Slovenians a penalty kick or free kick, give them another crack at scoring? 
Of course, maybe the Slovenian mob got to him and told him, whatever you do, the Americans can't win.  Sure, that's a possibility.  But if I'm a ref, and my daughter loses a finger if I let the American's win, I'd make some extra blown calls to make sure it wasn't too close.
Side note:  If this particular ref was biased, where are the other horribly Anti-American calls?  Did he make some horribly anti-Slovenian calls too?  Because if he did, then more likely he's just a bad ref.
The timing of this particular call is the one thing that I think conspiracty theorists have going for them.  That towards the end of the game, the guy made sure the Americans didn't win it.
But that's hardly proof of any conspiracy.  Circumstantial evidence at best.
 
 

Part of me thinks he might have seen something that happened before the play even started.  Or in his mind this was a 'make-up' call for something that happened earlier in the match.
In any case, justice was served by Slovenia not being able to advance.This has to be heartbreaking to Slovenia, especially after leading the group (by 2 points!, even if illegally gotten) to not be able to advance.  True Karma.

Well we don't know what the ref was thinking, because no one knows what he called.  Which is just idiotic, as many have already pointed out.
Good points about the differences between the Joyce call and the Slovenian call.  You're right, they are not the same.
Let me be clear:  I am not saying there wasn't bias, or that there wasn't malicious intent and forethought.  There may very well have been.
What I take issue with is the assertion that it is 'obvious' that the ref acted with malice and forethought.  That it is a 'given' that the ref was trying to exert influence on the game.  That human error could not have been a factor.
The Joyce call, and the selective attention studies, show the inherent fallibility in human perception.  Those are but 2 examples of something for which there is a mountain of evidence.  People blow red lights because they don't see them.  They remember things that didn't happen.  They see something out of the corner of their eye that's nothing more than a neuron firing or a shadow moving.
Even if this ref is proven to have tried to change the outcome of the game...  It doensn't change the fact that a mistake such as this is well, well within the boundaries of human error.
To be frank I'm surprised that egregiously bad calls like this don't happen more often.

Undoubtedly refs can be biased. 
Helping to counteract the incentive to exert influence on the game, are the repercussions for doing so.  The public shame and humiliation of Donaghy, along with the loss of his livlihood, strongly encourages others to NOT do what he did.
Which is what's so problematic with the Slovenian call.  No accountability.

Well like I said, the fallibility of human perception is proven.  It's not even a debatable point, IMO, that a call like this can be blown wihout any malicious intent.  A wealth of research and precedent shows this.
To point at a freeze frame and say, 'See!  See!' misses the whole point.  The argument that's being made is that we know the ref's mind.  And we don't.
If we ever have quotes from the ref, if we ever have an inkling of money exchanging hands, if we ever have any reason to suspect foul play besides an egregiously bad call, then the conversation changes.  And those things should be sought out.  The real crime here is that doesn't seem to be happening.

Tommy Smyth called the English goal that wasn't, 'The worst call in Futball I've ever seen'. 
The play-by-play commentator said it was 'Far, far worse a call' than the American goal waved off against Slovenia.
So.  If you think the the American call was a conspiracy to alter the game, just because it was an obvious call, then the England non-goal has to be a conspiracy for the same reason, yes?  Any call that is that obvious must therefore be due to bias or malice.
I'm not a huge soccer fan.  And these blatant bad calls certainly reduce my interest in the game, as Doc indicated they do for him. 
We want the game to be fair, and we want the call to be correct.  That is why it boggles why baseball and other sports don't implement replay more.  We want to know what really happened.
The other thing that has me scratching my head.  Why only 1 on-field official in soccer?
The field is huge.  There are 22 players on the pitch.  How can ONE official be relied upon to call the game?  This boggles me too.  Ya, I know there are 2 linesman.  But for crying out loud, basketball has 3 refs on the court, and it's a tiny fraction the size of a soccer field, and there are 1/2 the number of players.
Seems to me like Soccer could do with a refereeing make-over.

Here about the officiating at the World Cup.
Here's a list of the countries that got jobbed by the refs, going by that article:
Argentina - Brazil - US - Switzerland - Ivory Coast - France - Italy - Australia - England
Don't really see a pattern there.  If there was a systematic effort to exert influence on the cup, it doesn't seem to be showing up.
It's possible that in all of these instances, bias or malice was the culprit.  It's possible that it was the cuprit in some but not all of the instances.  If bias or malice is the source in some, the most likely would be the most egregious calls, of which the England call is probably the worst, followed by the US, followed by the others - some of which were pretty awful.
More likely, IMO, is this is further evidence that refs are human, that they don't see everything that happens on the pitch, and that the system of refereeing in this sport needs to change.
 

Apparently have a lot in common...