Though it took me a while to disengage from my former way of thinking, I’ve developed a very simple philosophy about this sort of thing. I call it “selective nihilism”.
What it comes down to is this: if you like a work, and think the story makes sense, then it ‘counts’ as being a real part of the overall story of that fictional world. If you don’t like it, and think the story doesn’t make sense, then it doesn’t count.
Your position will be far more justifiable if you can articulately explain (as much to yourself as to others) why you think something shouldn’t count, but ultimately it is up to the viewer/reader of any work to decide if the story is worth anything to them or not. If it isn’t, it can be negated, and thus dismissed from existence.
For example, many here (including myself) have decided that the prequel films do not conform to the events or storytelling logic of the originals. We have therefore decided to dismiss them and say they do not count. I personally do not believe that any amount of retconning, invented explanations, fan-editing, or other mental gymnastics can be successful in making them fit with the original movies, and since they are generally bad and irritating, not only do I never watch them anymore, I have actively dismissed them from my mind to the extent that they no longer influence my thoughts about the original movies in any significant way. In fact, I have very nearly succeeded in forgetting they exist.
If you find that a work cannot be entirely negated in this way (it usually takes a while to disengage completely due to emotional involvement in the story and characters), then problematic storylines can be relegated to alternate universes, while the “true” story can continue in your mind unpolluted by the unwanted elements. I tend to think of the new SW movies in this way: they are tedious sequels that can be shunted into an alternate universe containing the prequels and special editions, while the Thrawn books by Timothy Zahn are to me the ‘true’ sequel trilogy that follows the original unaltered films.
I am still occasionally prone to feelings of resentment about the state of official Star Wars canon, but by adopting the philosophy I have described above, my enjoyment of the earlier works that I fell in love with can continue unabated and untarnished by the later foolishness. The only problematic thing about using this method is that it can be difficult to explain to other people: I usually avoid talking about Star Wars in more than a fleeting sort of way with people in real life (unless I know they hold similar views), because I dislike having to explain that while I love Star Wars a great deal, I am by no means a ‘Star Wars fan’. Just because something carries that name does not mean that it is automatically worthy of my time or consideration, or that I should have to think about any story concepts it may have introduced while thinking about the earlier works.