Ok, this post stems from an aversion to checking every card in every expansion (part laziness but mostly because I don't want to ruin the surprisesof the cards I haven't seen in play yet). Basically I want to consolidate all the non-specific cards from all of the expansions into the base game, but I want to avoid adding any that are tied to an expansion. Now I am assuming that aside from the obvious 'special' cards (eg. Innsmouth Look), Mythos cards and Encounter cards for expansion locations; the rest are non-specific and can be combined without 'uh-oh, this card relates to Dunwich' happening for example. In other words the decks from expansions that do not require an expansion to be in play. Did that make sense? 
Cards That Are Specific To Expansions...or not?!?
This is a little problematic because there are six mythos cards that either add monsters to Dunwich streets or removes monsters from Dunwich, and they are all gate bursts for Arkham locations.
Nyogtha said:
Ok, this post stems from an aversion to checking every card in every expansion (part laziness but mostly because I don't want to ruin the surprisesof the cards I haven't seen in play yet). Basically I want to consolidate all the non-specific cards from all of the expansions into the base game, but I want to avoid adding any that are tied to an expansion. Now I am assuming that aside from the obvious 'special' cards (eg. Innsmouth Look), Mythos cards and Encounter cards for expansion locations; the rest are non-specific and can be combined without 'uh-oh, this card relates to Dunwich' happening for example. In other words the decks from expansions that do not require an expansion to be in play. Did that make sense? 
I don't recall the specific encounter, but I ran into one the other day in an Arkham location card that referred to either Dunwich or Kingsport. I only play with one board expansion at a time (I was playing with Innsmouth) and the location event card was useless. Note that the card was for an original board location, but referred to a different board. Something like "get a ride from the train station to Whatley Farm."
Most Arkham locations can be mixed together and if the one is drawn that refears to another board then just shuffle the deck and draw another. There are only like 1 or 2 cards that do that. I take all of the Arkham location cards from every expansion, cept the Dark Pharaoh unless using the exhibit (because i dont play but with one theme). I take all of the Gate cards and shuffle them together also. I always play with the Injury and Madness cards, The corruption cards, just encase an encounter tells me to take one, and the epic battle cards.
All spells, allies (cept the one that has to do with exhibit items), common and unique item can also be mixed together.
Things I leave out are game components that taylor to a certain board or theme. For instance with innsmouth: I use the aquatic mosters, dagon, hydra, and the innsmouth board and mythos cards.
For the Dark Pharaoh I add the exhibit items, the locations, the mythos and the barred taints and blessings (sorry cant remember the names), I also use the Dark Pharaoh for the Herald. I only use the Arkham board.
For black goat i add the Black goat I use the dunnwich board and all of its components.
Hope that helps.
My location decks for playing regular base Arkham are 21 cards each. So even if that one rare location that refers to another twon pops up, i can still just reshuffle, chances of it appearing are already slim.
I only own Black Goat, Dunwich, Pharaoh, and Innsmouth, and Kingsport (but I don't use kingssport cept for locations and epic battle)
Thanks for the feedback guys. That all tallys with my thinking on the matter too, much appreciated.