Here's a new feature that I think will come in extremely handy. The new Compare Sets page (under the Sets menu) lets you pick two sets and see which parts they have in common and which parts from each set are unique.
First, simply enter two set ids (or MOC ids). You can use the magnifying glass to bring up a search box if you prefer. Click the Compare button when ready.
A simple side-by-side comparison of the two sets will be shown. First a summary of the number of parts they have in common. Click the "Show Parts" link to toggle display of these parts.
Under that, there are two columns of parts. The left column shows parts that are in the first set but not in the second. The right column shows parts that are in the second set but not in the first.
Not much to it really. Enjoy :)