The standard BibTeX bibliography styles impose fixed ideas about the capitalisation of titles of things in the bibliography. While this is not unreasonable by BibTeX's lights (the rules come from the Chicago Manual of Style) it can be troublesome, since BibTeX fails to recognise special uses (such as acronyms, chemical formulae, etc.).
The solution is to enclose the letter or letters, whose capitalisation BibTeX should not touch, in braces, as:
title = {The {THE} operating system},
Sometimes you find BibTeX changing the case of a single letter
inappropriately. No matter: the technique can be applied to single
letters, as in:
title = {Te{X}niques and tips},
If your document design specification requires a different style of
capitalisation, you should acquire a bibliography style that doesn't
enforce BibTeX's default rules. It is definitely not a good
idea to enclose an entire title in braces, as in
title = {{TeXniques and tips}},
though that does ensure that the capitalisation is not changed. Your
BibTeX database should be a general-purpose thing, not something
tuned to the requirements of a particular document, or to the way you
are thinking today.
There's more on the subject in the BibTeX documentation.
This question on the Web: http://www.tex.ac.uk/cgi-bin/texfaq2html?label=capbibtex