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Here are a few ideas and tricks I've learned.
1. Set up Genre as a tag-like column.
When you classify a book in two different genres, both genres will appear in the field in the list of books. However, the two different entries will appear separately in the tag browser on the left. For example, I classify most of Edgar Rice Burroughs as both Adventure and Science Fiction. There's an "Adventure" option and a "Science Fiction" option under "Genre" in the tag browser, and these books pass the filter for both.
2. Create a series-like Subseries column.
Even if you don't expect to use it immediately, one day you'll come across a set of books that are part of a series-within-a-series, and if you already have the column set up, you won't have to pull your hair out trying to figure out how to deal with it.
3. If you're used to organizing your books by folder, create a text column to store a hierarchy.
I have a custom "Path" column for this. (Although in hindsight, that's not the best name because it can too easily be confused with the file path)
After creating the column, add it to your list of hierarchical fields by going to Preferences -> Look and Feel -> Tag Browser and choose it in the drop-down list for Categories with hierarchical items.
This will allow you to organize your books within the library in a structure that mirrors the way you originally had them on your hard drive. For instance, if you had a book in Fiction/Classics/Mark Twain on your hard drive, you would put Fiction.Classics.Mark Twain in your hierarchical field. You can set up a Save-to-Disk template that replaces the periods with slashes if you ever want to export your library back out to your hard drive and keep the hierarchical structure.
4. Use virtual libraries instead of separate physical libraries whenever possible.
There are plenty of good reasons for maintaining separate physical libraries, but unless you know exactly why you're separating your books like that, chances are you can use Virtual libraries to accomplish the same thing, plus you have the added benefit of being able to group all your books together if you need to.
I recommend creating a field specifically to identify which virtual library each book goes into. Make it a tag-like field just in case you decide a book needs to go into more than one library.
6. Install the View Manager plugin.
Why? Because it's the answer to half a dozen questions you haven't even thought to ask yet. View Manager is to sorting and column arranging what Virtual Libraries are to filtering. Once you have a decent-sized library, you'll find yourself jumping back and forth between two or three sorts, and View Manager can make the process instantaneous.
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