I do not know of any accurate price guides.  The only accurate rarity guide I've ever come across is at www.NintendoAGE.com. ; If you search for a game it will give you an accurate rarity rating (1-10) for the game, box, and manual.  I hate how many people use Mike Etler's list because it is so outdated and inaccurate! 

eBay.com pretty much commands the value of NES games these days.  So if you're looking for the value of a single game I'd check the completed listings there.  Unfortunately there are no rarity/pricing guides that I know of that are condensed and ready to be printed out.

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What makes the nintendoAGE list so accurate? Did whoever made it have information about game production run numbers or something? Or is was it just compiled through being in the scene, knowing what is harder to get and making educated guesses?

I can tell you this much. All of the sources are wrong when they say Zelda and Zelda II gold cartridge games are very common. Loose yes, but they are nearly impossible to find FACTORY SEALED!

Any game is hard to find factory sealed.  When dealing with factory sealed games Zelda is one of the easiest to find.  People will still pay a shitton for it though because it is highly desired.