[Plugin: Breadcrumb NavXT] Any way to hide certain categories?

There are no methods built into the plugin to do this. There are ways to extend the plugin to do it, but at the moment I can not recommend their use as there will be a bit of a reorganizing of the options for 4.0 which break all of them (as a side effect, not intentional). The crux of the issue is you end up having to specify the category you want to use on each post. Most forms of doing this require an extra database query, which we are trying to reduce as they are often slow. The other methods require changing of code to add a post id, category id relationship for each new post.

Also note, with the advent of tags and custom taxonomies, there are very few cases where a post should be a member of multiple categories. There should be one “true” root through categories and other attributes are added through tags and custom taxonomies.

If this is for the site you had the question on before, then there are some obvious categories that should actually be tags. Such as:
Coming Soon
Featured
In Theaters
On Blu-ray and DVD

The only main categories that should be categories are:
Movie News
Movie Reviews
Game News
Game Reviews

All posts comfortably fit under these four classifications, the four other categories only add additional descriptors to this. Some of which are temporary (“In Theaters”, and “Coming Soon” are definitely temporary).

Thanks for all the input, WordPress has changed a lot since we started using it, so I’ll def look into changing categories to tags in the future. The one problem that has prevented me from making the change and has kept me using the system we currently use is another plugin called Similar Posts. The plugin works best when set to relate similar posts based off the same tags. If I were to make the change you suggested, then the output of the plugin would be far less accurate and most posts would not share anything in common besides the fact that they were news or reviews. But thanks, will still look into the changes in the future.