We changed one of the Sheep tiles to Brick. So there are 3 Sheep and 4 Brick. (Instead of 4 sheep and 3 brick.)
We changed the number tiles to give a more balanced board (obtained from internet somewhere). This swaps the I and O, and the R and L. So the order is A B C D E F G H O J K R M N I P Q L. (You can write the new letters on the back of those to make it easier.) This means the numbers are 5-2-6-3-8-10-9-12-5-4-8-11-9-4-11-6-3-10.
We put the desert on the inside ring or middle. To do this leave the desert out of the hex tiles, place the outer ring, shuffle the desert into the remaining tiles, and place the rest.
Play with Helpers of Catan cards. They are an excellent addition, can't imagine the game without it. - We changed the "Development Card Choice" to not choose from the top 3 cards. We interpret "Force Trade" that you pick which 1 or 2 players ahead of time, and trying to trade and not being able to still counts as use.
Yup, all these in every game (with the exception of desert, you can put it in normally just to mix it up). The new number order is much better, it takes out the overpowered spots.