Zotero is in my opinion the best solution to citation management available. It's a firefox/xulrunner based solution for collecting and maintaining bibliographic data and it's associated full text. Zotero has a cloud based API but also an internal (largely undocumented) Javascript API. I find the JS API much more interesting than the cloud API due to having total control over my data (and works offline etc etc...).

Two frustrations I've had with a lack of good alternative to the msword integration code, and problems with interacting with the internal…