I recommend saving those up for the store (not that you can spend them elsewhere). I like to get Theme Decks: when you first get a theme deck you can take it through the single player mode to get a "free" booster (just takes 12 wins). While you don't have to do it right away, I don't think you can buy multiples of the same deck and still pull that trick off (you can buy multiples of a deck, sometimes useful when it has certain cards in it).
Make sure you take the free theme decks they provide and finish the single player mode for some goodies (trade locked boosters, tokens and a few card unlocks as well, I think). I like having more options for Theme Deck mode, but that is less critical if you can assemble a real deck ASAP. EDIT: Also note that while some items will stick around the store for a long time, others are short time offers! If you can keep a few thousand tokens on hand at all times, it is pretty nice. Even things like Theme Decks and boosters eventually disappear.
After that, each weak they will (eventually) put something less common and pricey in the online store. There is a Gift Set called "Ancient Powers", for example, that will be going up as soon as a glitch is fixed. It'll give you what the IRL version would have, but of course for the PTCGO. Really pricey though; probably 900-1000 tokens.
Other than that, just buy what you want; boosters means you might pull something instead of having to trade for it (and if you get something you traded for after-the-fact then you can still trade the non-locked version away), or you can get stuff you like (they have virtual sleeves and deck boxes) or stuff for your avatar.