It's unlikely that your outbound linking is causing your pages to be listed in the supplemental, rather than main index.
Adam, it may not be the outbound linking in itself that would cause Supplemental pages, but in addition to being considerate of the user experience, I'm thinking that it could possibly be contributing a little bit, but in a different way. Or to put it better, causing some lost opportunity with regard to PR distribution within the site.
I just went through all outbound links on my site, and found all of these situations. I try to check outbound links regularly, but I honestly can't say when the last time I checked was.
I have so many pages in supplemental that I'd like to restore to the regular index, and I'm wondering if this is contributing to the issue.
Andy, if not the links themselves, it might be having some effect by wasting PR on bad links that could be better used to pass more PR on to the pages of your own site.
The value of the PR passed on to pages linked to from a page with 5 outbound links is worth more than from a page with 15 outbound links. So aside from getting quality inbound links to increase "votes" and PR for your site (which is always a good thing to do) and improving the quality of user experience, if you go through and eliminate all the bad links you'll be giving more of those pages' PR linking power back to the homepage of the site, which in turn can then give a bit more PR to the pages linked to from the homepage.
Don't know if that makes sense, but why waste good "link votes?" Getting rid of the bad links can only improve the overall quality of the site, so IMHO it's worth spending the time.
[edited by: Marcia at 10:00 pm (utc) on Oct. 2, 2006]