I'm looking for experienced webmasters who understand the act of using silos and implementing a structured categorisation of pages in a heirarchy. It is standard to never link across silos but to link up and down within them, to not dilute the relevance and strength of those pages, however how strict are you in doing this? Should I then rel nofollow all of my sidebar links, menu links, footer links etc and only keep followed internal links where they should be to follow best practices when siloing?
As long as your links are at internal cycle of webpages, I don't see any problem about it. Say wordpress as example, the sidebar could be flooded with links but by default they are for internal linking especially the blog archive div. In Web 2.0, homepage and other major subpages should always appear on all the pages since it's more user-friendly and gives you SE robots more reason to crawl more and index more in your website.