ModCS
Warning
This site is defunct and ModCS is no longer supported. The project has been continued by Autumn as a feature of their Cave Story Modloader plugin, AutPI. The documentation for AutPI ModCS can be found here.
This is the official site for ModCS, a Cave Story modding utility, which's main feature is a Lua scripting API. The Lua API currently easily allows you to make custom HUD elements, easily modify and make NPCs, create custom weapons and create custom TextScript commands.
This project was started to give people a more accessible way to make advanced Cave Story mods, without having to deal with Assembly and the limitations of the original executable of the game. This was also started to give people a somewhat more legal way to make advanced modifications.
To get started you may be interested in the Getting Started section, which contains a brief overview of basic Cave Story Modding before getting into Lua scripting.