This is an example of an abstract that has been annotated to show the key components. I came across it online one day and found it to be incredibly useful, but don't remember who made the annotations - if this is yours, please let me know so I can credit you!
A lot of my work is focused on morphology-based cladistic analyses. These datasets can very easily get out of hand, so I use spreadsheets to keep organized.
I keep a spreadsheet version of my character list (top) to keep track of various details about the character (what is it, where is it, who first used it, has it been modified since, etc.), and so that I can easily manipulate and organize them.
I also keep a spreadsheet version of my working matrix (bottom), because it doesn't hurt to have a backup, plus it allows me to document more information than in, say, Mesquite. For example, I like to leave comments for myself detailing why I couldn't score a particular character for a given specimen, or to make note of when a character appears 'wonky.'