Originally written for Macs by Ian Patterson as early as 2000 (based on reverse-engineering of Oni's demo), OniTools was probably the first modding tool for Oni. Although a crucial early part of the history of Oni modding, it is now superseded by OniSplit and accompanying GUIs such as Vago.
Info and download (use link at bottom of page): http://oni.moltenstudios.com/downloads/ianpatt.php (Warning: Classic app; will not run on Intel Macs.)
OniTools was ported to Windows as WinOni: http://oni.bungie.org/res/utilities.html#winoni
An alternative program in Windows was OniTools.NET: http://ssg.oni2.net/subfold/download/OniTools_NET.zip (requires .NET 2.0)