One of the things I am pretty OCD about when editing is the timeline; specifically, sniffing out broken timelines and internal and external inconsistencies. For about half the manuscripts we select for publication (or at least seriously consider publishing), one of the first things we’ll ask the author for is a detailed timeline for the plot, and possibly, if there are plot points that depend on events that have happened outside the story proper, basic biographical sketches/timelines of the characters.
Obviously everyone writes differently. I, for one, have never in my life managed to outline anything. I just sit down and start writing, linearly, usually with an idea of an end in mind, but never of the middle of a story. When I’m done, I let the whole thing percolate for a while, and start editing from the start now that I know everything that happens (and possibly find myself having to resurrect characters I killed off in the first chapter because I ended up needing them later). I repeat that process several times until I have a final draft of a story. That said, between the first and second draft, I usually compose the Excel spreadsheet from hell that itemizes the entire timeline, so that if someone were to ask me, “When did plot point X occur?” I could answer without hesitation, “April 16th, 1976.” It’s not just helpful for editing a rough draft into something bordering on coherence, the spreadsheet also makes a pretty good cheat sheet, so that if, for instance, I mention a character’s death in the first chapter and later write about the character’s funeral in the eighth chapter, I need only glance at the spreadsheet to determine the date of both and make sure that my story remains internally consistent.
When it comes to editing somebody else’s work, I’m usually looking for a similar reference, especially when there are multiple subplots involved.