Comic books are unlike any other medium. The characters involve have the same history (generally speaking) for decades and decades. They die and come back, they grow older and younger, they travel from dimension to dimension. With this in mind, retcons are inevitable, in fact, they can almost be a requirement. Sometimes they're necessary to undo a particularly poorly written story (AvX should be retconned in the near future, for example), or bring a character back from the dead or obscurity. Other times they're simply done in order to streamline continuity, whatever the reason, there are few ways to get them right, and a lot of ways to get them wrong.  
  
 
#1.  The less obtrusive and/or contrived, the better.
A retcon that slaps the reader in the face and says "YOU'RE WRONG" will often not be received especially well. A good example of this is the "Secondary Mutation". Sure, it came from left-field, but it directly violate any laws of mutants. It was just something that hadn't been named before. There were always different elements and subspecies to mutations (See Nightcrawler and Angel) so this, while not presented before and a pretty major change, was not directly jarring to continuity.   
First X-Men is an example of a retcon that is so fundamentally flawed and quite frankly offensive that it should not be discussed in polite company. It served little real purpose, other than to sell comics (thus bringing this series into #4 territory as well), and muddled up continuity so badly that it defies belief. 
 
#2. The simplest explanation is often the best.
A good example here is the Mockingbird and Clint reconciliation that was later revealed to be a Skrull. This meant that Clint had actually made up with a Skrull, regardless of how little sense that makes. In fact, the entirety of Secret Invasion occurred in a similar fashion, until Tom Brevoort (someone who openly admits he doesn't read much) was forced to fill in gaps with what amounted to little more than stubborn guesswork.  
The reason it was decided that Mockingbird was a Skrull at this point in time, rather than merely replaced, revived and resuscitated after her "death", was because the drama of a Clint/Bobbi reunion was desired. That's fine, but what Marvel should have done is simply said that she lost her memory of everything before "X instance". This meant that rather than her Skrull pursuing a relationship that didn't make a whole lot of sense, she would have just forgotten about the two making amends. That way, we know that Bobbi had forgiven Clint, and despite her forgetting, the last 20 years of her existence wouldn't have been spent with her being bitter inside of a Skrull ship.  
 
In short, things like "they forgot" or "it was all a trick by a telepath" may be cliched, but they are cliched because they work. If you spend too much time on an intricate retcon, people will begin to think about it more and more, and when they do, they will find the flaws. You're screwing with history, there will always be flaws.   
 
This isn't to say that a level of sophistication can't be applied to a retcon, but rather, unless it's a huge, multi-layered event-style change, it's best to just go with the easy option. 
 
#3. Change the cause, not the result. 
When Hal Jordan was revealed to have been manipulated by the Fear-Entity Parallax, a huge sigh of relief was heard amongst the GL community. Their hero was not someone who suffered horrifying trauma and caused a massacre and almost the dissolution of reality, instead he was victimised for feeling fear, and thus being human. This was a good idea. Hal was taken advantage of by a malevolent creature that took his feelings of fear, despair and distress to monstrous extremes. It preyed on him, but it preyed on feelings that were still there.  
 
The problem with this retcon was that Johns and company weren't willing to let it end there. Hal was immediately absolved of all guilt, and forgiven by virtually everyone who wasn't portrayed as a prick. After the Zero Hour/Parallax fiasco, Hal was humbled and then tried to atone for his actions. This added an additional layer to the somewhat cocky, cowboy-esque hero, and brought him into a new era. Sure, he'd keep those characters that made him a fan-favourite to begin with, but he would always carry that doubt, but also the wisdom that comes with it.  
Instead, he was absolved of all sins, told it would never happen again, and got a clean slate once more. Right.  
 
#4. Avoid unnecessary retcons.  
Sometimes, though this is most often the case with characters that a writer is desperately trying to make popular with fans, a retcon will be brought in quickly and quietly. It might make for a huge deal, generally it's only done to illicit a smile form the reader, but these are often the most jarring.
Jessica Jones being the biggest social outcast at Peter Parker's high school, and having a huge crush on him is an example of an unnecessary retcon. While it seems cute at first, the reader is then left wondering, why didn't she ask him out? And if she was in one of his classes, which she must have been, otherwise how would she know who she was, and Peter didn't notice her, what kind of a jerk is Peter Parker? So the reader is left with these kinds of questions. 
A classic unnecessary retcon is the Mighty Avengers - Wasp preserved in subspace through the Avengers Mansion. Originally set up so that Hank Pym could work on a way to revive her, this was later scrapped for no reason so that the character could be revived in another way, and actually made Hank look utterly incompetent. 
 
#5. Conclusion.  
A retcon is usually a bad thing. That's not because the concept is inherently bad, but because most of the time, writers hurry to explain things in ways that satisfy them, without taking into consideration which characters they're screwing over. 

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After further review, I no longer really believe what I'm selling here. Too many terrible retcons to justify my saying they can be a force for good. In addition, most of the good retcons are really just a matter of "tidying up", than actively changing history. But this thing took me awhile to write, so I can't just delete it.