Does this really have an affect on the game besides the bounty hunters and the random crap gifts?

I think it will affect the ending, although I'm not sure because I haven't finished the game yet. In any case I believe some people will not give you quests if you're really good or evil, depending on their own disposition.

it does effect the end

Certain cities are only useful for certain alignments. A very good character won't be welcome in Paradise Falls.