should I fight to choose journal my work is submitted to? I'm a USA grad student in computational biology.  Starting 2 years ago, I tried to get paper X published, with very little feedback from my advisor, and after a year (!) in review paper X was rejected. Meanwhile, I was working on other projects, gaining experience, and drawing closer to graduation. My advisor then asked me to submit X to a kind of shady non-journal "proceedings" (he had some hook-up), and he didn't seem happy that I objected. Now, I hope to graduate in a few months, and with the benefit of my improved knowledge of science, I'm trying to get project X published again.  My advisor only cares about getting things out the door, not about the projects, and he has a connection to this Chinese journal (jmcb.oxfordjournals.org) that I never heard of. He is impressed  by their impact factor because that's how he is (I can tell they are gaming their IF.). He wants me to put it there, while I think a lower IF, less obscure journal would be way better. Additionally, it appears that very few institutions subscribe to this journal (my univ does not).

It's not a spam journal, but I never would want to submit there, and I feel that I should have some control over it as it's my work. But is it worth it to fight him on this, or should I just go along with it because he's the boss? I guess if it's easy to publish there, I should be grateful not to have to keep working on it after graduation? I do want to do a postdoc.
If the journal is junk, you should not publish there, period. So, the real question is: Is the journal as bad as you think it is or this journal is just not one of the top journals in your area but still a legit, reputable journal? So, confirm which of the two applies. How to distinguish journals has already been discussed several times in this forum. Check the editors, look their homepages if they mention their editorial work there, see who else publishes there and check some of the published articles.

In case this is actually a legit, reputable journal but still not top of the line, you should really consider if your work is actually as good as you think it is. It already has got a rejection and perhaps your advisor suggests some medium (and not top) journal, since he may believe your work might actually have a chance there. So, be open about this and ask him. What does he actually think about your specific work? Is it not good enough for the top journals? If he believes it is not, perhaps you should reconsider your stance.