Why try avoiding? I am going to use them for external affiliate links so I don't pass PR back to the affiliate site.
Yes you are correct, javeScript links do not pass PR. But it will be simpler and less code to use the rel="nofollow" attribute than javaScript.
Yes but some people use roll over images that are coded in javascript. They might not know CSS and are only using what there program made for them or whatever. So there is no real point in trying to use the nofollow tag because they want to keep there fancy roll over effects.
Another reason I wanted to use them was becauase I want to reduce the length of the url that pops up when you hover over the url. I believe this can be done. I have seen sites that when I hover over external links it looks like this: www."site link is on".com/link to this site.htm is that a javascript link?