I would say that perhaps the most powerful ones overall are a flowchart and a logic tree.
The flowchart helps understand the system works in sequence. Some people use them but only at a high level, but they can be done repeatedly at each level to get a deeper understanding of causes.
The logic tree is a replacement for the cause & effect diagram. It allows looking at cause & effect relationships in chunks, so you don't have to be thinking about so many simultaneously. And if you can show that one of the branches on the tree did not create the problem, then all the detailed causes below it go away.