It all depends on how powerful your characters are, and what sorts of things you think they can handle. Yes, the rules imply a certain amount of 'level playing field', which is fine if you are either a novice DM or don't really know the characters' strengths and weaknesses all that well.
Once a DM is comfortable with their ability to assess the party, I think you can throw the EL stuff out the window. Just put the characters up against whatever you think should be there. I'm all for balance from a campaign point of view, but I don't go out of my way to balance each and every encounter.
And I have not changed my approach with the advent of 3.x... Players are the same, and the situation hasn't changed that much to be honest. Characters still have the same resources they have always had, and to be honest, 3.x characters are far more powerful than they ever were in previous editions, so my inclination is to worry about balance even less than before.