in many games you are supposed to do things in a certain order, usually because some places are out of reach until your character got a new ability/item or otherwise advanced in the game.
For example: In Super Metroid you should get the High Jump before visiting Kraid. You need the high jump to hop onto a ledge that leads to him.
If a speedrunner finds a way to change the order (in this case: reaching kraid before aquiring the High jump by using a walljump), he has broken the intended sequence.
Sequence breaks are not automatically faster, and not every possible sequence break is good for speedrunning. Some sequence breaks can save you from taking unneeded detours, others give you strong abilities early that can save time later on, and they are used in speedruns.
Lower Norfair without Varia is awesome, too, if only because you can almost believe it was intended. If opening green doors from the wrong side weren't so obviously a glitch, that is. The placement of power bombs and super missiles is so good for farming, it's like they knew someone would want to CF down there.