Welcome to the world of citation managers, aka bibliographic management systems, reference management systems, documentation preparation systems.
Here's what they do:
In the boxes on the left are links to commercial and open source citation managers.
RefWorks is web-based, and is typically supported by academic institutions for all users. As an alumnus you can continue your account. RefWorks has over 3,000 citation formats to choose from, for standard styles such as APA or MLA, for societies, and even for specific journals.
EndNote is typically purchased for a single machine, but there is now a web version. Many engineering and medical types got started with EndNote early on. Preference seems to depend on what you are used to.
Because it is open source and free, many people are now turning to Zotero. Mendeley is also becoming popular.
Mathematicians and computer scientists like BibTeX and LaTeX, a document mark-up system for preparing bibliographies and papers, because they handle equations well. ACM Digital Library exports to BibTeX, as do EndNote and Zotero. Unfortunately LaTeX is expensive and has a big learning curve, and doesn't convert well to non-proprietary formats. If you are choosing a software, see which handles the special character sets associated with engineering the best for you. You can always do a combo of using RefWorks or Mendeley for creating your citation database and BibTeX for citing.
JabRef is based on BibTex.