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My preferred bibtex style file cites via author's initials. However, there are various texts which should be cited differently (for example, Elements Geometrie Algebrique should always be cited as [EGA]). I know how to modify this in the .bbl file that bibtex outputs, but then I have to do this for every file. Is there a way to do this from my .bib file?

+2  A: 

You can modify the .bst program so that it looks for an additional field, say shown-key, and if it is set uses that rather than the usual.

Charles Stewart
+3  A: 
Norman Ramsey
This is actually a fairly common convention, endorsed by Chicago: cf. CMoS 16.39. So at least some of the gods will let you do this.
Charles Stewart
"BibTeX uses one of the world's worst programming languages" - it's actually Not Bad, when its purpose is considered: most .bst files are easy enough to read. The main problem with bibtex, one that justifies "world's worst" is if your style calls for you to parse entries from your .bib file... But then tex is hardly pleasant for this kind of task.
Charles Stewart
I'd avoid "key" for something that is visible: I reserve such names as key, alternate-key, keys, some others do the same.
Charles Stewart
@Charles: As a specialist in programming languages with wide experience of simple postfix languages as well as more general programming languages, I stand by my claim about BibTeX. Oren would have done much better simply to adopt PostScript wholesale (although that might have required a little time travel). Good suggestion on `key` though.
Norman Ramsey
@Norman: Let me put it this way: I don't number the limitations of the .bst language among the main defects of bibtex. This is not to defend the .bst language as an example of how to design a concatenative language, where I defer to your superior knowledge.
Charles Stewart
@Charles: Thanks for that clarification. Finding defects in bibtex is like shooting fish in a barrel. http://packages.debian.org/search?keywords=nbibtex
Norman Ramsey