An easy thing to forget about TeX is that it tries to guess what you mean, and can get it wrong. In this case, I am talking about periods.
TeX interprets a period based on the previous letter. If the previous letter is a capital, like "D. Knuth", it puts a normal space in, thinking that you are giving an initial. If it is lowercase, like "I went to the store. It was nice", it assumes you meant a period that ends a sentence, which has about 1 to 1.5 spaces after it (depending on the justification needs and the style settings you prefer).
But what if you have a sentence that ends with, say, "which is why I like NINJAS." Here, the period ends a sentence. Or how about, "all of the misc. tools", where the period doesn't?
A quick way to check to see if you made an oops doing this in your source file is to run the two scripts:
grep "[A-Z]\. " *.tex
This checks for the first case, while this:
grep "[a-z]\. [a-z]" *.tex
checks for the second case.
To fix the case with the capital and the period, change "
NINJAS. " to "
NINJAS\@. ", to tell TeX to treat the period as a sentence stopper.
For the other case, with the lowercase and the period, change "
misc. tools" to "
misc.\ tools", to tell TeX to treat it as a normal space.
I strongly recommend that anyone who uses TeX or LaTeX should, at some point, read The TeXbook, by Donald Knuth, and find out what really goes on under the hood.
Thanks to John for giving one of the scripts and reminding me of this.