Hi Sighteer,
Just to add to some of James' comments, and specifically your question around references within CrossRef: When they originated, CrossRef accepted deposits that only contained metadata for the item to be indexed; however, in the past few years they have been trying to build links between items, and as such have started pushing the need for reference information as well (in fact, they now charge a
"non-linking fee" of $0.22/article).
Extracting and sufficiently marking up this reference information for articles was one of the primary goals behind the development of Lemon8-XML, and is something that we're working to incorporate into OJS (OJS 2.3 will contain an area for entering reference metadata, for example). Structuring this information in a way that meets CrossRef's requirements takes some effort, though we're hoping to use the technology from L8X to make it easier. You might want to have a look at this paper which describes these issues in greater detail:
http://journal.code4lib.org/articles/1011Hope this helps,
MJ