I have taken the existing Stella 1.2 source code from SourceForge, and combined it with the CPU emulation core from the pre-Stella 1.4 cvs source.
The resulting marriage resulted in what I'm calling Stella 1.2.wishbear -- I had wished for a long time that Stella would support illegal opcodes such as those used in Space Treat and Homestar Runner RPG.
You can get the sourcecode and application from my .Mac website http://homepage.mac.com/ps_inkling/stella/index.html. I'm not that good at making double-click installers.
I've been using it the last month with no problems; however, I've not tested it with every 2600 game ever made. If it breaks, you get to keep both pieces.
Hopefully, Stella 1.4 using the SDL library will be available soon.