The Theory: There is a Matt Cutts video on this topic (the series where he says, we have a question form so&so in everytown, country). He says that if the sites are similarly themed and you make it clear the sites belong to the same company, this should present no problem.
The Experience: I've had a network of related sites since 2002. First it was two sites, then three. Circa 2005 I can say unambiguously that this increased serps. Today I don't think the sitewide linking helps as much, but it is still the best you can do if you have a PR4 or better site to link out with. When we had a -40/50 penalty on some pages beginning after the Panda update on October 13, 2011. I undid everything I thought might be suspect. One of those things was the footer linking between the 3 sites. After the one penalized site recovered from the penalty i started putting things back in, including those footer links and a few other changes. One of the three penalized pages got re-penalized. Right now I can't say for 100% sure whether or not the footer cross-linking caused it or not.
I have a second group of two sites, 1 and 2 years old, that do the comprehensive footer cross linking on every page, and they are both top ranked in their niches (one is number 1 for every term i care about).
In any event, if the sites are related, even without search engines results, I get significant and measurable traffic and sales from the cross linking. So at least in some cases it is worthwhile even if you don't care at all about SERPs (and that is how Google says you should be making design decisions, right?). However, my experience suggests there may be good and bad ways of doing it (think about anchor text, etc.).
I think the best strategy today is to do what you suggest and link from body text and fewer rather than all pages.
The big issue is that your new mini-site site has no link popularity to pass along to your main site.
If you have a PR6-7 site to link to the minisite, it will quickly be PR4-5 at which point it will gather it's own links with no additional effort if it has high quality (meaning better than just about any other similar resource on the web). Then you will have a PR5 site to feedback to any other site you choose.