I think it depends on what you're doing and how you've measured it.
Using a pencil to mark,to cut accurately to length, I would mark so that the outside of the line was the length and cut to that - the very outside tips of the saw teeth against the out side of the line.
If marking with a knife, the inside of the knife cut is where the saw cut will be so it has to be measured accordingly.
When it doesn't matter so much about accuracy, deep scribe marks are fine to cut into the centre of: - Roy Underhill's grease box for eg., it doesn't matter how thick the lid ends up, it only has to fit it's box.