I posted this in another similar topic, but if you don't know how to play the game, the HS Trainer Kit would be an ideal starting point, as it teaches you the ropes as well as having two copies each of two of the most sought after (and pricey) Trainers in the game at the moment for only around $13.
I'd also suggest getting one of the Black & White theme decks, as they contain the updated rules, as well as having decent cards in all of them.
Along those lines, the sets I'd recommend investing in are HeartGold/SoulSilver, HS Triumphant, and Black & White, as they have most of the cards that many top decks will use. Avoid Call of Legends, as many of the cards in that set are reprints of cards found in the other HS series sets, and the unique cards in the set can be obtained fairly cheaply.