Generally, it is a good idea to delete whatever is possible because the uploading (or upgrading through cPanel) process may not correctly overwrite an existing file and that may cause problems later.
DO NOT DELETE these folders and files:
wp-includes/languages/ folder–if you are using a language file, do not delete this folder;
.htaccess file–if you have added custom rules to your .htaccess, do not delete it;
Custom Content and/or Plugins–if you have any images or other custom content or Plugins inside the wp-content folder, DO NOT delete them.
DELETE these Files and Folders:
wp-* (except for those above), readme.html, wp.php, xmlrpc.php, and license.txt; files; Typically files in your root or wordpress folder. Again, don’t delete the wp-config.php file.
wp-includes folder; If using a language file remember don’t delete the wp-includes/languages/ folder
wp-content/cache folder; You only see this folder if you are upgrading FROM WordPress 2.0.
Step 4: Run the upgrade script
Visit your blog’s Upgrade Page (http://yourdomainname.com/wp-admin/upgrade.php) and follow the instructions that are displayed.
Step 5: Reactivate Plugins one by one
Activate your plug-ins, one by one, at the Plugin Management Page. Check if everything works as expected.
If any plugin does not work, deactivate it and then you might contact the plugin author to encourage the author to upgrade the plugin.