I would like to see an open source alternative to mobigen.exe, but the original may be "good enough". It takes an OEB document (html with a OPF file), or plain HTML, and produces a MOBI file. So the way to produce MobiPocket books is the same as for several of the older e-book formats - start with an actual OEB document and then convert it to the required bastardized commercial OEB variant.
MobiPocket has consistently put all its Desktop resources into Windows, so mobigen.exe is Windows only. My guess is that it would take about a day for someone with its source code to get it working natively under Linux and OSX, but I perhaps it is incredibly Windows-centric (i.e. it might take a week to port) and perhaps MobiPocket only has Windows programmers.
In any case, it is a command-line program that runs using wine under Linux (and probably also using wine under OSX). Wine isn't that hard to install and use under Linux, I don't know how well it works under OSX.
For an earlier related discussion (with many links), see
MobiPocket TOC using mobigen