How many templates do you have? Generally, packing everything into index.php is a bad idea. I’m not 100% sure if you’re overloading it too much or not, since I can’t see how your theme is fully structured, but it’s something to keep in mind.
You have so many other templates that you can use!
Posts use single.php
Pages use page.php
Categories us category.php
You’ll want to look at this: http://codex.wordpress.org/File:Template_Hierarchy.png