ReadCube is really great for finding papers. Their enhanced PDFs makes it very easy to get to cited papers and they are really good at finding papers that have cited what you are reading. So for reading through the literature it is my favourite. It sucks when you have to cite papers, though. I have tried to use its citation tool but it only works with Word and you are screwed if you want to sort the cited references alphabetically.
Papers is better for citing, especially when you want to use BibTeX. It works well with most editors and it is very easy to export your library to a BibTex file. It isn’t automated, which is a pity, but it is reasonably good.
So what I really want is to use ReadCube when collecting my papers and then use Papers when citing them.
Here’s a little trick for automatically importing papers to Papers when you import them into ReadCube.
You can tell Papers to watch for PDFs in a folder and automatically import them. So if you go to preferences you can tell it to watch the ReadCube files. It should be in your Documents folder and be called something like ReadCube Media.