I am happy since moving from Mendeley to Zotero. I like that I can store my pdfs on dropbox, and use Zotero on many different PCs. Mendeley's insistence on absolute paths to the database prohibited this.
Zotero's use of Google Scholar to extract metadata from pdfs made it easy when starting with several thousand pdfs.
I use Zotero (+ownCloud for storage) as well, a bit quirky at times but has all the functionality I need. Don't know how good the standalone program is, I only use the browser plugin+libreoffice plugin and occasionally the dreaded ms-office plugin as well (if not working with latex).
Standalone works very well too. Can recommend.
Zotero is pretty decent and Open Source.
A killer feature of Mendeley for me was its ability to extract metadata from PDFs. I remember that I could not find a comparable functionality in Zotero last time I evaluated it. Is there any way to do it now?