I also agree with gillette888 regarding have a running total of the cost of my collection.
I would be pleased if the ability to mark or have multiple sub-collections was included. This enables marking which cards are in which binder, or which deck rather than just knowing I have a playset of a certain card but no idea where all of them are among the 3 binders I have, various evolving decks and the overflowing uncommon/common boxes of doom.
As an aside, having recently returned to MtG this has really helped me review the decks I'm building, figuring out curves and such. My husband stopped mid-stride walking past me the other night while I was building a modern deck to ask what program I was using and then help me with the deck allowing him a chance to play with the site himself. Not only did he think it cool he was wowed at seeing such a good program he hadn't stumbled upon himself yet.
The only other thing on my wish list of eventually would be awesome is an app to access the collection to change my collection during trades rather than take notes and come home. One can dream.
If any of these are here and I'm just too new to the program to have found them, please tell me.