I generally buy in person from the reputable big box retailers like Target and Wal-Mart, as 95% of the time, the cards they sell, even the after-market repackaged ones, are legitimate. I also buy from game shops, bookstores, and hobby shops I know have the official boosters.
Online, I've generally bought from eBay sellers with good reputations. I've not given the major online sellers (trollandtoad.com and the like) a go, and I've yet to actually buy any from Amazon or the sellers that use it, either. I know there are a few people that come around here every once in a while that have some experience with the legitimate online retailers, so they can give you more details on which one is better, but the reputable ones I can think of off the top of my head are trollandtoad.com, pokeorder.com, and tcgplayer.com.
Any sellers in particular you were looking for references on?