In my blog template, I have a "top five articles" section on the menu bar that displays the articles' title and an excerpt. I have it the same way on the main part of the template where new posts appear. If I submit a new article and add it to the "top five articles" section on the sidebar, the same instance of the article title and description will appear twice. Will Google penalize a website for this?
It shouldn't be a problem. As long as you make sure you have UNIQUE content in the main body/content are of each page, then having the same text in the header, footer, and sidebar areas shouldn't be a problem at all.
not an issue at all. all blogs have excerpts on the home page and main article on the inner pages. however, it will be lot safer to use canonical urls to avoid duplicate content issue. just google for "canonical url" and you will find all you need to know