There are ways to keep your link partners as long as you do it the smart way and if you do not have thousands.
Link pages are what gets people hit by google. If you do exchange, you need to do it from internal pages that are actual content. link pages (link farms) are a violation of T.O.S. It is considered a linking scheme. You can read this thread to get a better idea of proper link exchanges.
Seo for Link Building and Web Traffic. You can have your cake and eat it to.
Concerning supplemental results, Matt Cutts stated directly that the best way to get a page out of supplemental results is to get some high quality links pointing to the page in question. You have to remember that google wants pages that are "popular" and link popularity is the biggest factor that google uses to rate a pages popularity.
Directory links: These will not get you punished. paid links will get you punished anywhere, not just on directories. I always use directory links to diversify IP addresses of inbound links. they are not the highest of quality and have little seo power in the links alone, but when doing social bookmarking, articles, press releases ect... you have a limited number of sites that will pick you up, so you get repeated links from directories and Press Release sites and this can cause a problem with lowering link values because of repeated links from the same IP's.
Now, if you are writing on popular subjects you may get a lot of republishes on other sites, but how many republishes do you think you would get about sewer cleanup, or something like nails (for building purposes). This is just not interesting content that the majority of the population would be interested in. But if you have a travel site, you may get loads of republishes.
So diversifying ip addresses is important in a small niche market.
All of these changes are factual , but google has been warning people for months or even years about the coming changes in algorithnms.
The basics of this story is do not take the "popular" road and the shortcuts.
Take the road less traveled and it will make all the difference in the world.
Hope this helps,
Jim