Recently I installed the simple, but beautiful Suffusion theme by Sayontan Sinha. This theme is using the funtions.php file extensively, the same place where my shortcode definitions were stored. Sayontan will probably fix this in the near future by including a custom functions.php file from another location. I also used some PHP code in two sidebar widgets that was executed by the Exec-PHP plugin.
I thought, why not use a plugin to define shortcodes and execute PHP code snippets? I couldn’t find one, so I wrote one myself. You can find it in the WordPress repository as Shortcode Exec PHP.