My MMPB Trek books are shelved by series, in order of publication, each series having its own paperback bookcase. TPB and HC books have another bookcase, in which they are shelved by publication date. TNG is in the dining room, near my computer desk. TOS (I don't read DS9 or VOY) are kept in the 'Trek room'.
At the very bottom of my TNG bookcase, are my CSI and James Rollins MMPB, shelved by publication date. There's also a few books I have purchased but not yet read, but when they've been read, they'll be joining the collection in the 'library', with my parents' books.
All of my parents' MMPB are shelved in another room to themselves (the 'library'), in nine home-made PB bookshelves and nine boxes. Currently, they are in whatever order my parents had them in, but when I find the time, I shall be rearranging them by genre and author. Same with all of my non-Trek books, which shall be joining them, eventually.
The Trek reference books are on still another shelf, easlily available to me when on the computer. They're in no particular order, though.
As for cataloguing, only my parents collection is in the process of being catalogued in a spreadsheet database, since I'm not really sure exactly what I've got. There's about thirty years of PB collecting there, but I know I've got lots of Doc Savage, Nick Carter, sci-fi, westerns and mystery. I've only gone through the nine boxes and two of the bookcases and I'm up to 638 books.
You know, the most disturbing thing to me was when I cleaned out my parents' house, one of my relatives questioned why I kept the books. To me that's just the damned stupidest question.
DES
Save one life and you're a hero.
Save 230 million and you're a Starfleet officer.