I cheat slightly sometimes. The jointer gives as true a perpendicular planed edge as it's setup allows (readjust with set-square every time I pop it back on the bench) but even a 100th of a degree can cause (I forget the true word for this) hydroplaning of surfaces under the pressure exerted by clamping for glue. I find you get it less if you lightly rough edges with 80 grit, dampen with a cloth, rough with 120 and then lightly apply glue to both edges, spreading with a credit card for consistency. Waiting a minute before applying both edges and clamping seems to cause a little less shifting when bringing up to pressure.
I have no scientific proof of why I do this, or any evidence to say it's better than any other method. It works for me on porous wood like mahogany, and it doesn't seem to cause excessive buildup of glue line. As with anything, your mileage may vary!