The main alternate rule I use is from Pyramid 3-83 "Knowing Your Own Strength" which brings the Strength Attribute back into line with all the others. I highly recommend it as it makes things a bit simpler in character creation. Or at least it has with my group.
Another is that HP is based on the weight of the character. Mass correlating to how much damage one can take actually works quite well.
Finally Ranged weapons use Per instead of Dex. Knowing several people who shoot on a regular basis, they have repeatedly said that its breath control and a steady eye that are more important with guns than nimbleness. Or at least if you don't plan to follow the "spray and pray" method of shooting.
These are the big ones that most of my builds take into account. When time permits I will do a second, vanilla build.
