As far as I know, rarity only matters in the bazaar. (Rarity is not used to excuse unbalanced cards)
Rare cards in the bazaar are marked with the large warning that flashes up.
I still think some visual difference is a good idea, if only to tell the newbies that the card they're looking at (or even better, have just won) is something they can't buy/couldn't have bought from the bazaar. Also, I'm not sure if the bugs in the warning system have been fixed. (I remember reading that if selling, say, a Titan causes a nymph to move into the same slot, the nymph can then be sold with no warning -- but now I can't find the thread in the bug-report section.)
Wizards of the Coast has two ways to indicate (different types of) rarity for MtG cards: they make the expansion symbol black (if the card is common), silver (uncommon), gold (rare) or fiery orange (mythic rare); and they put either a black or a white border around the card frame (usually black in the first set that includes the card, and white thereafter). The latter type of rarity matters mostly to collectors, since the border doesn't affect how the card works in the game -- although it does mean that a player trading with a collector would be able to get more cards in exchange for a black-bordered card, or more money that he could use to buy new cards.
As for Elements, the lower-right corner of each card has something white with a black shadow -- either a column capital, lightning bolt, or ATK|HP stats. Could this something keep its current appearance on the common cards, but be black with a white shadow if the card is rare? (I don't think Elements needs the second type of rarity. At least, not until it has a trading system, or something that serves a similar purpose.)