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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 bibliography style, or to the way you are thinking today — for example, on a future occasion, you might find yourself using a different BibTeX style with different capitalisation rules.

There’s more on the subject in the BibTeX documentation.