Two questions regarding the use of Categories in each of the items.
1) Is there a way to set a default, so that when the Category Quick Find tree is launched, the data will be show collapsed?
2) Is there a way to display a different value to the user than what gets entered into the database (i.e., display "Apple", but store "Granny Smith Apple". This is to allow the same category to appear under different parents).
1) You can get a collapsed view and have it be the default, but you first have to select the view on each client. (Possible with a bit of user education...) Go to the Administrator Console, open "Presentation"->"Views"->"Service call Category" (or whatever category field you want to modify). Then create a new tree view here, and under the "Other" button there's a checkbox for "All expanded" that you can turn off.
Close your client and re-open it since the views are cached at initial launch. Then open a Service Call and click the "Quick Find" for Category. Change the view at the top to the view you created above. From then on, the new view will be the default for that client.
It's not optimal, since you can't force it out to be everyone's default, but it is workable.
2) Mark's right that there's no way to do this immediately through the client. You could try using other innocuous characters like underscores or spaces to allow for the different categories and then ignore those characters when reporting, but that's a bit messy to maintain I'd imagine. Personally, I'd say that if something fits under more than one category, you may want to re-visit your categorization scheme and try to make the broad categories overlap a bit less if possible.