We also have used custom fields to track some more internal stuff.
In order to find these tickets by their external reference, one has to search in a custom field.
Our users report this to be cumbersome, as they have to do a "search issues" -> "select issue type" -> "search" (so that the custom fields for that specific issue type are show) "enter the search criteria" and finally search.
It would be much easier if they could just type this into the quicksearch.
If this slows things down too much, how about makeing this configurable?