I've done some searching, but I've yet to find an unambiguous answer for this. I want to upload some scientific research papers that are crucial to the content of my site. I'll be making some income off affiliate advertising, but the main draw will be my original content, not the papers. Is this OK?
You need permission from the authors of the research papers, before you can upload them to your site. If you don't have their permission you would be infringing their copyright and they could take action against you.
To be more specific, you need permission from the copyright holder. If the papers have been published in a journal the authors probably do not hold the copyright.
What if I don't have any ads and I don't make any money off the site? Is it OK to upload research papers then? (many other people are already doing this on their sites)
No, not having ads does not make it okay. Other people doing it also does not make it legal, and how do you know they don't have permission to use the research papers? Papers that are in open access publications (they would use that term - open access) allow for use in this fashion. If the papers you want are published in this manner then you can use them, as they have permission built in. If not, then you must seek permission from the copyright holder.