Moving CiviCRM from Windows to Linux
If Drupal you need to update the temporary files folder under Administer - Configuration - File System, and possibly in the files table you might have paths using a backslash that need to be converted.

Also even for non-drupal for the windows to linux direction pay attention to capitalization for any file paths. Linux is case-sensitive but windows is not. 

And your civicrm.settings.php file may need updating for backslashes and capitalization.

File permissions and file/folder ownership also tend to be more varied on linux. You may have to grant permission to the web server (see e.g. Are there recommended directory ownership and permission settings for CiviCRM files?)