The top two teams go directly into the Champions League group stage. The third and fourth place team go to the third qualifying round, where they play a 2 legged qualifier where the winner advances to the group stage. So 2nd place essentially gets a double bye compared to 3rd, so the difference is fairly significant.
One exception will be if Arsenal wins the Champions League (they're in the final against Barcelona), they go directly to the group stage as holders and will take the spot of the 4th place team, who will go to the UEFA Cup instead.