I don't think there is a best or easy referencing system, they are all fairly frustrating in their own way! I haven't used endnote (couldn't get on with it) and have used refworks. This was the software available through work and also uni. I found it very tedious inputting data manually although importing from pubmed etc was a doddle once I worked through the help. It did give me Harvard output in word format so I could just select the relevant references and create essentially a word file for inclusion into my thesis document. It worked well for me!
Not used referencing section on word 2010, may have to look at that one myself. Would be interested to see any other comments on this.