Is it a good idea to include working papers on Curriculum Vitae? I am a senior undergraduate student and looking to apply to PhD programs. I am doubtful whether I should put my working papers on my CV alongside the already published works. I don't want to exclude them because I think my work in progress are more important than the published works. Will listing a separate section for working papers, with a side note on where do I intend to submit them be good?
Work in progress can be a good indicator of both interest and ability. I wouldn't exclude them and a separate section for it would be good. I doubt that a lot of undergraduates are in this position, though my perspective is the US. 

Saying where you intend to submit/publish them is a bit speculative unless you have already published in those venues. But it is more likely to help than hurt as it shows you have a plan. 

But in general, giving your work in progress shows an active research trajectory that might be carried directly into grad school if the circumstances are right.