When possible, I look for the first place in Tana"ch that the Hebrew word is used (assuming, of course, that it is a Biblically used word.
"Sefer" is mentioned "early" in the Torah in [Breishit 5:1][1]Breishit 5:1, "This is the 'sefer' of the generations of Adam (man - humanity)" - My loose translation esp. of the word "Adam", in the is context.
I linked to the Mikra'ot Gedolot version, intentionally, because each commentary has a slightly different explanation of the word 'sefer'.
Seforno (I have a feeling that his name originated from 'sefer', BTW, though I don't know what the connection is.) translates it as "story".
Rash"i translates this as "accounting" or "counting" - i.e. connected to numerology.
In terms of using "sefer" for the names of most books, either of these terms may apply. Most works called "sefer" has some form of "accounting". Sefer Minyan Hamitzvot (from Ramba"m) is an example. The mitzvoth are counted / assigned a number. Why not just leave the word "sefer" out? Perhaps, but, maybe for someone who didn't know what the book was about, isn't it nice to know that by saying "sefer", now I know this book has some sort of "counting" or a method of assigning a number to the ideas in the book?
The 2nd definition - "story" could also mean "lessons". I.e. - the "stories" being told are not like a bedtime story where it's just nice to hear. These are meant to be examples, morals, or lessons taught on how to behave and conduct your life properly. Sefer Chafetz Chaim has lessons and examples / stories (a few) to teach you individual lessons on how to conduct your life.
Incorporating from a comment - if it were just called "Chafetz Chaim" you would have some general idea that this book had something related about "desiring life" or improving how you live. By saying "sefer", you have some idea of the structure - it's telling me some stories.
(Note - Rav Kagan is called "The Chafetz Chayim" because it was custom to name people after one of their most notable seforim that they wrote, not the other way around. The book is not named after the Rav!)
Granted, I'm sure that my explanation may not apply to every book with the title "Sefer", but, probably a majority. If you think of any that may break this rule, I'd like to know. But, IMO, that may be one of several exceptions to the trend. [1]: http://hebrewbooks.org/pdfpager.aspx?req=9597&st=&pgnum=92