Chemistry - Program that simulates basic reactions in organic chemistry
As you mentioned, there've been quite some attempts on CAOS (Computer-Assisted Organic Synthesis), such as
- WODCA from the Gasteiger group
- CHIRON from the Hanessian group
- LHASA from the Corey group
I might be awfully wrong, but I think they were/are all closed source.
But you might want to have a look at OSET, an open source Java project on which Ivan Tubert-Brohman worked some ten years ago.
A few more links to those listed above:
- Peter Ertl's synthetic accessibility score (SAscore)
- ArChem - also called Route Designer
There was also a lot of hype a few years ago about an effort called Chematica, but I have not seen an actual shipping product (commercial or otherwise).