The ramifications of alignment was a biggy, especially whether you went magic or technology. There's the whole wizards city (or whatever, I haven't played the game in far too long) that if you went technological you was pretty much outright banned from and it was a bitch to gain entry.

Again your reputation for good or evil also helped later in the game. If you was evil (and had the reputation of a killer) you could intimidate much better because you had the right charisma traits attached to you character.