Bad Relationship with Master's Supervisor: Missing Reference I'm in the situation that I'm completing my master's research degree and I'm in the process of applying to several applied mathematics / computational science programs. 

Here's me complaining:
I do research for a collaboration and most of my research work has been for the calibration field of the experiment. My relationship with my supervisor has been less than good. He originally lied about the kind of research I'd be doing and because I'm in a program where you pick you supervisor before entering into the program, my impressions of him where very preliminary and not reflective of his concern in students' interests. My current impression of him is that he's a career administrative academic, his involvement in the collaboration is merely to appear involved in research despite not being in charge or overseeing any research that comes out of the collaboration itself. In the past, I've voiced my concerns with him about needing to be more clear and direct about the work he wants from me for the collaboration, only for him to be incommunicado for several months, that is until someone in the collaboration needs something he promised he'd get for them. At that point, he comes to me telling me to get something to him in the next week, saying I haven't been doing anything meaningful; over working me. The research I do do often does involve different people from different institutions, but it's never enough to be a reference for me as my involvement with other collaborations is somewhat scattered
End of complaining.

I can't switch advisors because for one, he's the assistant chair and would and would have impact on if I should be kept in the program if I request a change.   And if I did end up switching, the department would likely delay my defense, which I cannot afford. I'm stuck with my advisor and project till my thesis. Which I can deal with, it's the lack of reference in my applications that worries me. Now, I have quite a bit of research as an undergraduate where I'm getting letters of reference (all research experience). But will the lack of a letter from my thesis research screw me over?
I was in a similar situation last semester. My advisor had me join a research project, but gave me little to no information regarding said project. He told me that I would be working with honeypots, and it wasn't until my first day that I realized he meant honeypots in the cybersecurity sense and not literal honeypots. Although I was relieved to find out that I wouldn't have any bee stings from my research I could tell that I wasn't going to get any help from my advisor. In fact, he was away attending conferences for most of the semester, and rarely responded to any of my emails. 

Here's what worked for me that I think will help you. You need to post up outside your advisor's office. When he finally comes in, you need to talk to him about how you're feeling and your current situation. I don't want to say confront him because I think that's too strong of a word, but he needs to know that he is not pulling his end of the bargain. Or, if you can't switch advisors, just ask him if there is anyone other resource that you can talk to, to gain more knowledge about the project (but on the low make this your "advisor"). 

As for the references, I would talk to the other people that you are collaborating with. See if they can help you with a reference letter. Or try to find other people who have worked with your advisor and see what they have done. I hope this helps and wish you well on your future endeavors.