My webpage has about 8 links at the top (8 sections) and links on the side that vary with every section.
A few months ago I put my side links at the bottom of the page (they were previously underneath the main navigation) and saw one of my internal page's ranking increase for a specific term.
The problem was that underneath the main navigation, I had this elaborate table for a page heading, so when I did a site command, all my pages except the home page were in the omitted results. So I changed it back again, lost the internal page ranking (wasn't important), but got back all pages out of the omitted results.
Now about a week ago, my pages are starting to go into the omitted results again. So last Friday I put this elaborate table down the bottom, leaving an <h1> tag at the top. The side links are still at the top though.
I am hoping this will sort out this omitted result problem I have. The pages look the same as they were before, it's just I am altering the CSS and HTML code to put content nearer to the top.