Outer Limits hosts many of the Cape Town V:tES tournaments and is a strong supporter of the local V:tES community. Their V:tES stock is somewhat limited but what they do have is generally reasonably priced.
Somewhat more expensive than Outer Limits but they usually stock more cards.
Most moderately serious players end up purchasing cards from overseas. Overseas stores local players have had good dealings with include:
Sells boosters and sealed decks to people outside Europe.
An eBay store that sells cards as singles and in small batches. Good for filling in those annoying holes in your collection. Occasionally has special offers that are worthwhile keeping an eye out for.
Unfortunately now closed. :/