the <code> generates a monospace text in the tiny font size.
You might want to enable the option "Large Code Font" in your Display Settings.
Generally, <code> or <c> tags should be used for all code, sample input, output, etc. They do not interpret any other tags or PerlMonks [...] links inside them, and they provide the [download] link. (Update: Note that <code> tags are a special feature of PerlMonks and are not the HTML5 <code> tags.)
<pre> tags are just HTML formatting tags; they no not prevent the interpretation of other HTML tags or PM [...] links inside them, and AFAIK get no special processing from PM. The only advantage they have is that they support Unicode, while <code> tags unfortunately do not; but you still have to escape all the <>&[] characters inside <pre> tags. (Combining <code> and <pre> doesn't make sense.)