I always take a clean approach - where possible, I keep the WordPress core files and plugins unmodified to allow easy future updates.
Some solutions that I implemented:
- adjust URL routing for better SEO
- programming CSV imports / exports, cross-database queries
- developing multiple-steps survey forms / calculators with advanced data administration
- programming widgets, adjusting user-profiles, extending parent themes
- plugin extension / configuration - WPML, CForm7, Gravity Forms, ACF, Shopp, W3TC, SEO plugins, MailChimp, Mandrill ..