I do both. Originally I had it all by alphabetic (and series as some related series have multiple names). Then it got to the point that when I was in the mood for anime and went to look at my collection I really couldn't find anything. I'd think, I want to watch horror, but then I'd have to scan the whole thing or remember all the titles I owned that were horror related.
That's when I spent a few hours redoing my shelves. I have 2 large DVD cabinets with sliding glass doors holding in my collection, so you can imagine the work I had to do to reorganize it. I redid things by major genre (Fighting, Magical Girl, Horror, Space Opera, Reverse Harem, Harem (things only got put into harem if it had no other major genre to speak of) and the like...ending in miscellaneous for everything left). Some major series like Tenchi Muyo and Sailor Moon got their own sections as did major artists like Studio Ghibli and Makoto Shinkai. Never split off my Matsumoto collections but he is essentially hslf of my Space Operas anyhow.
For the most part I had everything grouped then picked shelves. Everything is separate (I have a ton of bookends so that was easy enough) so no runon genres when I have 2 or more genres to a shelf and then everything within the genre gets alphabetized. Series go with the first season, no matter what the names of subsequent seasons are, and that goes for related series too (Outlaw Star and Angel Links for example get placed together). Now I never have problems finding anime when the urge takes me and I always know where everything is.
I also maintain a word file of my collection organized exactly the same and I keep an updated version on the cloud so when I'm out or at conventions I can easily look up what I have at home and not buy the same thing twice. Sounds odd, but it has made life so much easier and I haven't rebought an anime by accident in years lol.
My best friend however does not maintain her similarly sizable collection in any order at all. She sent me pictures a few years ago. Just trying to read the titles off the shelves was a nightmare. But she keeps track of it in her head just fine so the more power to her. I am lost when looking at her collection lol.
As sn aside @Illusion of Terra I think things will pick back up come January. From October thru December is generally hectic for most people due to the holidays. Family comes first, right? Even for me this holiday season has been insane.