As a Christian, if you're speaking of the God of the bible....then this is an extremely difficult question for me and one that has been debated since Jesus walked the earth and it will continue to be debated until He returns.
I am confident that when you ask "does God take sides in wars" you mean the wars of men.
The scriptures are clear that He took sides in the old testament. In Deuteronomy 20:16-18 he told the Israelites to kill everyone within the cities that He would give them as an inheritance. He wiped out those people, however, because they were wicked and because they did abominable things.
Our God is not a whimsical God. He doesn't kill for the fun of killing. You will see time and again it was for punishment...yet people twist it & make Him out to be a murderous God.
In the new testament we see that it says in Romans 13 to, "Let every soul be subject to the governing authorities. For there is no authority except from God, and the authorities that exist are appointed by God. Therefore whoever resists the authority resists the ordinance of God, and those who resist will bring judgment on themselves."
This seems to be problematic. The United States exists today because of a rebellion against the British authority. If all governments are established by God and yet these governments have war with one another then what's the cause? Were there not Christians on both sides of the water?
God is sovereign. He does as He pleases but, again, He has a plan. His plan seems to revolve around the fellowship that He desires to have with His creation. His creation has rejected Him and so bad things are happening and have been happening since the day we first turned from Him.
Through Christ He is reconciling us back to Him so those born of Christ have a great dilemma when it comes to war. At least I know I would have a dilemma on my hands if I were called to war. The Holy Spirit in me propels me to "love" and to "save" instead of destroy. Jesus said, "I did not come to destroy man but to save him."
I am not saying that there is not a time for war because Ecclesiastes declares that there is a time for everything under the sun...a time for peace and a time for war. I would not, however, relish the responsibility of deciding when war was appropriate on this earth.
Lastly, we see war being waged in the book of Revelation. A Spiritual war that culminates in the ultimate demise of Satan.
I revel in that war.