Shift-clicking on the "?" button in NEI recipe gui when the vanilla crafting grid is open pulls items from the player's inventory and makes the recipe complete when all the items are present.
I know it's easier said than done but it's a 'must have' kind of enhancement.
Most modded crafting tables (including TiCon) also have support for this thanks to NEI Addons (hint hint @bdew).

I'll look into adding support for the basic workbench in NEI Addons. Taking items from the additional inventory is all kinds of pain in the arse and there's a good chance i won't get it to work.

\o/

@bdew definitely don't attempt to do additional storage support yet...I'm in the middle of refactoring the GUI, and the last thing I want is for you to get things integrated nicely, and then have my refactor break stuff. See issue #11 (comment) for more info.