Looking at how the Bible itself uses the phrase Word of God is interesting. In the New Testament 'Word' comes from the Greek Logos, and is used in three different senses:
First and the main sense is to mean Jesus as God's fullest expression of himself in human form (i.e. in the opening of John's Gospel - "In the beginning was the Word, and the Word was with God and the Word was God", substitute "Christ" for "the Word" in that passage and you will see what I mean).
Secondly it was used to refer to the preaching of the church, e.g. Peter delivering a sermon.
Thirdly it refers to Scripture, and usually to the first five books of the Old Testament. Don't forget that when 2 Timothy 3:16 ("all Scripture is God breathed") was written, some of the books that ended up in the New Testament did not exist, and the Canon of Scripture (i.e. which books the early church saw as making up the Bible) wasn't finally decided until the 4th Century.
So the phrase "Word of God" means God's self-expression, primarily through Christ, but also through the teaching of the church and the words of Scripture. This does not mean to say that Scripture is therefore something that has to be taken as literally being words from God, rather it is a lens through which we can learn something of God.
I hope that is helpful.