Would you exchage a cover page link for two subpage links if the other site is stronger (e.g. 50 backlinks vs. 200 backlinks, both sites are ranking good)? Is there a general rule for this situation telling to never do such an exchange or must each single case be treated different? What's your opinion? --- Steve
No! You need to do like for like, otherwise you are losing out. Usually the home page has more PR and weight rather than inner pages.
I would always choose the in-content subpage links. For the most part, homepage links mean blogroll links, and unless it's from a quality site, it doesn't help too much.