At first sorry my bad english, i hope you understand what i mean.
Ingame Equipment Planer
A additional Character Window where you can place items from item links or databases like lootlink or Atlasloot. in a summary window you should see the stats and bonuses of your current and the difference to your desired equipment. (like the rating buster Stats Summary)
You could add a comment to every slot for example "Got to go to Mechanar to get this item". This way you dont have to crawl everytime thottbot, Atlasloot etc. to Check out where you can get the item.
Items you Finaly found, should be dyed in green, items you still need should be dyed in red (i mean the icons from the Item Slots).
And of course you should save your desired equipment/comments. :)
I was thinking of something just like this last night.. layout could be simple, looking like the JewelCrafting window, cept instead of collapsable catagories for gem color, just have them as item slots. You could add items by link, or if possible as you said, have Atlasloot support. Added items then could have comments, or if atlasloot support, list of which instance, heroic or normal, and which boss.
I dont know anything about mod programming or i'd take a stab at it, but it seems like the functionality/layout would be pretty simple.. anyone trying something like this? or would like to take a stab at it/