This comic is what made me think of this:
I was filing it away after reading it just recently. And after reading it, I realized that this comic has WAAAYYYY more to do with War of Kings, than it does Secret Invasion. In fact, it's pretty much the set-up issue for War of Kings.
Now obviously if you keep your comics in alphabetical order, it would go under "Secret Invasion." But then, what if you want to go back and read the War of Kings story again (BTW, if you haven't read War of Kings, you really need to get on that. Marvel cosmic goodness at it's best!), and it's 5 years later? You didn't remember that the prelude issue is "Secret Invasion: War of Kings," and you think you have the entire story with the main mini-serieses.
What do you guys do? In situations like this would you just group that with the rest of the War of Kings stuff (I did), or do you HAVE to have your collection in alpha-numeric order no matter what?