Catman,
Sorry to hear your about experience with travel agents. Luckily, I have found a heavenly travel agent who always makes sure I get the seats I like, enters my upgrade requests correctly, bills the right accounts for the different types of travel, books my car and hotels correctly AND does not charge me a fee when I'm booking free tickets (eg. 2 for 1 promotions). She is even taking on the task of arranging the travel of 80 registrants who will be attending a conference I'm having. What a brave soul!!

I think that trick is to find the "right" travel agent for you.