I received my PhD in 2009 and my adviser will not provide a good recommendation for me. This is mostly because we have fundamentally different approaches to science, and in retrospect I see that I could have avoided a breakdown in our relationship if I had been more deferential.
At this point, I leave his name off of my list of references, but I suspect that a diligent potential employer might call him anyway. I would be willing to discuss any concerns that were brought up in such a call - indeed I think that doing so will help me to find a good fit in a new position - but I do not know if I should, or how to state this fact in my job applications.
I am currently finishing my post doc, and one recommendation has been to take another post-doc so that I at least have two supportive references from postdoc advisers - and that the additional publications will place less weight on recommendations. Still, others have told me that not having a good reference from my adviser is a kiss of death.
How can I most effectively handle this situation?
I also had a falling out with my PhD supervisor but managed to secure a good postdoctoral position in spite of it (I'm told the letter of reference provided by my PhD supervisor was "very concise", but I was lucky that my skillset was rare and urgently needed by the group I joined).
When applying for positions at the end of my postdoc, I did not use my PhD supervisor as a referee, but instead used my postdoctoral advisor and two other senior academics with whom I had worked during my postdoc. My postdoctotal supervisor said that it might look odd not to have my PhD supervisor as a referee, but in fact, it wasn't a problem. It did help that my postdoc work was very collaborative, so there were several people who knew me and my work very well and were prepared to speak well of me. If your postdoc has been shoter (mine was a 3 year position) or if you have not been able to develop collaborations with other academics during your postdoc, it may well be that another postdoctoral position would help. If your PhD supervisor is well known and well regarded, it might also count against you if you did not get on (in my case, my PhD supervisor was obscure and was thought odd by most of those who knew him). Regardless of all these considerations, if I were you, I would apply to both faculty positions and attractive postdoctoral positions, and see how you go in practise.