The single biggest change made to World of Warcraft in patch 3.1 was the addition of dual talent specialization support. Glyphs are now bound to talent specs, and the player can swap between them at will. You must be out of combat, and switching talent loadouts will drain all of your mana/rage/energy/runic power. Get more info on dual talent specialization.
Besides that major change, there were some minor ones added as well, particularly regarding professions. In general, professions that previously required the player to complete a quest to learn the next rank (ie: Cooking, Fishing) have had that feature removed. The quests that used to teach the next rank as a reward will now grant a special item or recipe instead. Additionally, Cooking, Fishing, and First Aid is no longer learned from books - Instead, the trainers have done their reading and can now teach you themselves.
Another notable change is that gathering professions can no longer fail. This eliminates a lot of wasted time, as well as makes everything a lot more realistic. I mean, think about it. How can you fail at picking a flower? If anything your clumsiness would completely destroy it, not make it pickable again.
Since patch 3.1, items purchased with special currency, ie: Emblems of Heroism, Emblems of Conquest, etc. Can be returned to the vendor for a full refund within two hours of purchase. No doubt this significantly cuts down on the number of tickets GMs have to handle now.