Visibly.. Without putting them inside anything the general ways to display that I've seen are:
-Benches [Don't work so well with the smaller books though]
-The new carpet pieces. The end pieces. You can't raise them but if you place them on top of books they'll still 'lock down' when you double click them.
Goodman's Rune library is a good example of that.
-Make a public 'reading room.' Lots of tables and chairs with stacks of books in various piles.
You can use book shelves [the empty ones] and stack some so that they look like they're on the shelves.. Then set the shelf to public and have more inside.
Boxes - The wooden ones that players use for lockpick training.
Wooden engraving tools used on them can separate the books by writer or topic. I generally use the trough display case idea with this.
[Place two gozas, raise them up. place trough underneath and lower the gozas to cover the water.]
Cute display idea including benches w/ baskets.
[Screenshot is of Elisa's house]
Bookcase Idea