It's best to avoid changing the original files to make future upgrades easy.
Customize smarty templates, css styles and icons
Please see: Customizing Themes, edit templates and edit css
Customize JavaScript
Add your custom JavaScript to
styles/stylename/custom.js
or
styles/stylename/options/optionname/custom.js
Customize language files
Add your custom language strings to:
lang/**/custom.php
where ** is the language code.
More info: i18n
Customize profiles
Please see http://profiles.tiki.org
Customize the code overall (new features, etc.)