Is it a negative that my PhD research has been in several unrelated areas? I'm a PhD student in Computer Science. Long story short: I do not have a good relationship with my advisor. I don't trust his guidance or his ethical integrity. Therefore, I am seeking external advice for my situation.

During my PhD I got one paper accepted in a first tier conference, two papers accepted in a second tier conferences, and other papers published in workshops and minor conferences. I have one journal paper accepted. 

However, not all the work is on the same topic but it is scattered among three, mostly unrelated, subjects. Now my PhD is ending.

Is it negative that my work has been on three unrelated subjects?

(I cannot find a topic that allows me to merge all my results in my PhD thesis, I have to leave out at least half of my work.)
To the degree that you do have a PhD thesis and some other work (that, more over, has been published), I would say it is a positive thing, not a negative one. It is a good combination of "breadth and depth" as one comment has put it. The general advice I have heard many times for long-term planning, is "the ideal is to try to distinguish yourself in two fields inside a discipline. One -everybody tries that. Three -and your image starts getting blurry". Or something like that (and with the caveat that "fields inside a discipline" may not mean the same thing for different disciplines).