Depends what you need. Search for the parts you need most importantly and then go for the ones with the highest quantity and see what other parts they have that you may need. It isn't an exact science but I feel pretty good about how I've managed to work the system. Note that generally speaking in Lego terms 10¢ per piece or less is the range you want to be in. Lego sets used to sell for that much but now it is more like 11¢ or 12¢ per piece from them so if you can do better than that benchmark on bricklink it is probably a good deal.
Some parts are obviously going to cost more, this is more for when you are about to make your final checkout to look at the number of parts you have vs. your total.
"Ya gotta remember, Soryu's a brutal thug, ain't got no finesse like Shinji."