Stopper Knots are imperative to keeping a line from slipping through all of its blocks and pulling out. The idea is to have the line pass through the blocks as it makes its way to the cockpit, and then stay in the cockpit.
Lets take a jib sheet as an example, the sheet comes off the winch and slips out of your hand. If there is no stopper knot, the sheet will pull through the fairlead and flap wildly in the wind as the jib flogs. You can't use the engine to bring the bow into the wind since the sheets can foul the prop. This whole dilemma could have been thwarted by using a stop knot, which would have kept the bitter end of the sheet from passing through the fairlead, allowing a much easier recovery.
While it may seem logical to place the stop knot at the very end of the sheet, this is not advisable. Think about it, the sheet pulls away because it was under tension. Now the stop knot is jammed into a block and you have nothing to grab onto to pull it out! You needed a winch before because the line was under tension, now you have no way of getting it to the winch and it's still under load.
To make matters easier, locate the stop knot ahead of the bitter end. If the sheet were to pull away, you want to have enough tail to reach the winch and allow you to place a few wraps around the winch drum.
This does equate to a rather long sheet, you factor in the length that you would have needed, and then add the distance from a stop knot to the winch. This should be the length of your sheets.