Another key piece is the naming of the file. If, like most here, you have a directory structure of Publisher/Title (I would like to add Publisher/Title/Volume for some titles), the next step is how the folder looks when you open it up. Unless you rename files that you download, then your folder will be a mess. Folks use a million conventions, and you need to pick one that you like, and rename the files as you download them in order for them to sort properly.
I use, for example:
1940-12 Jungle Comics 012 [c2c 68p] JVJ-BB.cbz
...where the date is first to make sure that books sort if you have more than one volume in a folder (think Blue Bolt, for example). I make sure that I capture whether a book is c2c and the page count, in case a book is incomplete and gets later upgraded. Plus, I always try to hang onto the uploader's tag in the name, because sometimes it is not contained in the file itself, and could be lost. Otherwise, how could I locate the high quality scans later by guys like Cimmerian, OE, Lofty and others?