Here’s a great big table that compares all the thesis reference tools that I have played with. Hopefully it will help you to choose which one suits you best.

 DocearEndNotePapersReadCubeRefWorksMendeleyZotero
PriceFreeFree/$250$79Free/$55 per year$100 per yearFreeFree
Free optionhappymonkeyhappymonkeysadmonkeyhappymonkeysadmonkeyhappymonkeyhappymonkey
Cloud storagesadmonkeyhappymonkeyhappymonkeyneutralmonkeysadmonkeyhappymonkeyhappymonkey
Organise .pdfshappymonkeyhappymonkeyhappymonkeyhappymonkeysadmonkeyhappymonkeyhappymonkey
Citation plugin for Wordsadmonkeyhappymonkeyhappymonkeyhappymonkeyhappymonkeyhappymonkeyhappymonkey
Annotate/highlight .pdfshappymonkeyhappymonkeyhappymonkeyhappymonkeysadmonkeyhappymonkeysadmonkey
Search databases for new papersneutralmonkeyneutralmonkeyneutralmonkeyhappymonkeyhappymonkeysadmonkeysadmonkey
Access your university library system to automatically download paperssadmonkeysadmonkeyneutralmonkeyhappymonkeysadmonkeysadmonkeysadmonkey
Text search your own papershappymonkeyhappymonkeyhappymonkeysadmonkeyhappymonkeyhappymonkeyhappymonkey
Recommendations based on your papershappymonkeysadmonkeysadmonkeyhappymonkeysadmonkeyhappymonkeysadmonkey
Share references in a private grouphappymonkeyhappymonkeyhappymonkeysadmonkeyhappymonkeyhappymonkeyhappymonkey
Public sharingsadmonkeysadmonkeysadmonkeysadmonkeysadmonkeyhappymonkeysadmonkey
Social network componentsadmonkeyhappymonkeyhappymonkeysadmonkeysadmonkeyhappymonkeyhappymonkey
Windowshappymonkeyhappymonkeyhappymonkeyhappymonkeyhappymonkeyhappymonkeyhappymonkey
Machappymonkeyhappymonkeyhappymonkeyhappymonkeyneutralmonkeyhappymonkeyhappymonkey
Web browsersadmonkeyhappymonkeyhappymonkeysadmonkeyneutralmonkeyhappymonkeyhappymonkey
Linuxhappymonkeyneutralmonkeyneutralmonkeyhappymonkeyneutralmonkeyhappymonkeyhappymonkey
iOSsadmonkeyhappymonkeyhappymonkeyhappymonkeysadmonkeyhappymonkeyneutralmonkey
Androidsadmonkeysadmonkeysadmonkeyhappymonkeysadmonkeyhappymonkeyneutralmonkey

It is safe to assume that I have messed something up in this table, please post corrections in the comments and I will get it sorted.