Havlen, I find myself in this situation now. My agent passed on one of my first SF novels, explaining that it didn't rock his boat. He suggested rewrites and said that I was free to send it out myself. I did, and hooked up with a Canadian publisher that did small offset print runs (1,500), but they had very limited distribution in place. We both agreed that sales here would be primarily driven by the author, as so commonly happens with small press. They seemed legit and had a good backlist, Amazon and all that. I have other books that my agent is sending to the majors.
So, in answer to your question, I believe that a small publisher who has some type of footprint in the industry can be seen as a legitimate credit, of course. The problem arises when and if a major excepts one of my books and desires to examine my past publishing record. The area that they will most likely scrutinize will be overall sales. And that could be the most damaging factor of all. They might frown on the fact that I've sold hundreds instead of thousands of copies. On the other hand, large publishers are well aware of the limitations of small press and really don't hold that against the author. So in the long run, a legitimate small press sale might be seen as a stepping stone for a debut novelist. That's how my agent explained it to me.
It's when you get into subsidy, coop, and obvious vanity presses, where this would become a problem--publishers who are not known for real editing, original artwork and book store placement. I just turned down a contract from Blu Phe'ir publishing because they wanted production costs on the back-end of the deal--royalties would be paid to the publisher until costs were recouped. WATCH OUT FOR THESE STEALTH PUBLISHERS, AS WELL AS THE BLATANT SUBSIDY AND VANITY OPERATIONS. THE DEAL BREAKERS ARE HIDDEN IN THE WORDING OF THE CONTRACT ITSELF. STUDY, STUDY, STUDY, AND SEEK ADVICE FROM THE WATCHDOGS.
Our Yog, James McDonald over at Absolutewrite, has often told us that being published badly is worse than not being published at all. That, of course, is open to interpretation. What he means by that can also include small publishers who have made the "bad" list and have a less than stellar reputation. So it all does depend on who is taking you to print
Not answering for John here...just relaying some experience.
Tri
Chris Stevenson