For example Mendeley, Endnote...etc. I have recently used Mendeley because it is free and easy to use. It pleasures for me to hear your experience with such programs.
I use Mendeley and it has been fit for my purpose. I keep adding articles (manually) onto the Mendeley Desktop and syncing to cloud on regular basis. I have over 400 documents and the MS Word Plugin helps me with my own MS Word articles and thesis.