For what it’s worth…
Yahoo is crazy unpredictable for me. I did the paid inclusion route awhile back only to have all but one site rejected. Luckily they refunded the money, no harm done.
But as far as non-paid goes, its still whacky. Some sites get indexed, get the positions they deserve and hold them well. Other sites with very similiar SEO related quality will get indexed but are almost blacklisted from day one. To make things even more interesting in the Yahoo puzzle, some sites can be in the Top 10 for a period of time, then they are gone for awhile, then back to Top 10 and back and forth forever.
This is based on first hand experience with my own sites, not conjecture. Just today one of my pharmacy sites was #6 for a competitive one word keyphrase for about 2 hours and then its gone again. This cycle has been ongoing for me for about 6 months with no end in sight to the sillyness. When Yahoo favours you its all good, but it doesnt last for long.
I have not seen any evidence of affiliate sites being targetted specifically. I’ve tried making some sites look as non-affiliate as possible ( hiding aff links via php scripts etc.) and it makes no difference at all.
Bottom Line for me: Yahoo is a nice bonus if my sites stick around for awhile, but Google is still more reliable despite its own issues.