Star Rod

A very advanced tool named Star Rod, still actively developed. It can edit pretty much every aspect of the game, including maps, battles and more.

The tool can be downloaded here.

Mario Mache

A tool made by skelux. Originally titled Origami 64 and later renamed Kirigami 64 is a tool to edit battle formations text and more.

The tool can be downloaded here.

Hack Rod

A very interesting tool. It's quite similar to Mario Mache, but has some advanced features like having the power to edit store items.

The tool can be downloaded here.