From Greyhawk to Garweeze Wurld (the difference is subtle I know), Faerun to Krynn, many of us have a favorite world to host adventuring parties. Perhaps, that world was the first D&D book we read, or we liked some aspect of it better, dragonlances or spellfire, mega-dungeons or underdark. Whatever the reason, most of our custom worlds draw heavily from these famous locales.
One of the guys in our Wed. gaming group was relating a story from a Star Wars game where they "killed" Darth Vader. My first thought was why did the GM allow that to happen, then I thought, why did he even put the game in that timeline? The first answer is obvious, he was a decent GM and gave his players agency to do what they wanted. The second answer is more interesting...
We obviously hold dear our childhood memories, I love Transformers and still have about 100 or so, some in their original boxes and I enjoyed the recent TF movies, despite the liberties taken with the original story and personalities tied to the various characters. For some reason, we can accept these changes if the budget is big enough, but we can't handle it when our friend's do it. Why is that? I can't speak for all gamers, but generally speaking, gamers are smart, diligent and respectful of the source material, yet fundamentally flawed in their approach to "the rest of the world."
So why run a game in our favorite world and favorite timeline, knowing that the players are eventually going to *dink* with something big? Well, we are most familiar with it, we don't have to do a lot of work (since we've already done the work of reading the stories) to build the world and we know what is going to happen - or at least *think* we do.
So my suggestion to you new GMs/DMs/STs is don't run (or ruin) a game in your favorite world and your favorite timeline, leave that to the game developers and authors. Use their stories to build your world's background or set up stuff yourself to make those stories your world's future.
You will get far more satisfaction from figuring out how everything fits together, how all the governments work, how the ecology came to be doing it yourself. And, if you spend enough time, and get it polished well enough, you might even consider publishing it, becoming one of those people who really does get to decide what happens in a beloved world.