I do enjoy Shadow Era, and Hothead's Kard Combat is excellent as well, but my new favorite deck-building card game on the App Store is Ascension, based on the real-life title by Gary Games. There's a lot of similarities to the great card game Dominion, in that you build a deck up as you play the game, rather than having to rely on a pre-built deck. As you add new summons to your deck and "slay" monsters, you earn honor from a limited pool, eventually trying to finish the game with more honor than your opponent.
The game is well-balanced, and while strategy at the beginning of the game is pretty simple, it really ramps up as your deck is established, with different summons both affecting the cards you play and what kinds of powers you can earn as you go along. The cards are all hand-drawn, easy to read and look great. Once you figure out how to play (there's an extensive tutorial to teach you), games move along at a solid pace. It's an excellent card game, and quite original in terms of how it's balanced and how it plays. And of course Game Center integration and asychronous multiplayer add a few solid selling points as well.
Ascension (subtitled Chronicle of the Godslayer) is available for US$4.99 as a universal app. If you are into these types of card games at all, definitely check it out.