What is exactly meant by "research experience" in grad application? I'm confused by what the term "research experience" actually means in a PhD application. The following examples come into my mind:


working as research assistant with university professor 
publishing research papers in conferences
work in R&amp;D division of company (industry research)


Do all examples of the list above count as research experience? Or which ones do? If so, what are they?

Which ones are more important and provide competitive advantage for getting accepted to good university?
I would say all of those count as "research experience".  Which ones will be most valued depends on the nature of the program you're applying to, and the exact nature of the work you did.  In general, though, the more independent your work was, the better, and the more generic it was, the worse.  So if you were a research assistant but all you did was photocopy documents, that will not earn you many points.  If you were a research assistant who, e.g., conducted experiments, did fieldwork, participated in lab meetings, whatever, those will be worth more.  If you actually contributed to the writing of papers or presentation at conferences, even better.

As a rule of thumb, the more that what you did was something other people could not have done (i.e., it required your special expertise, not just "more hands'), the "better" it is.