Joe Coder has an article about it on his web site.

Here’s his overview:

In the Old Testament are the military campaigns of Israel inconsistent with being led by a just and loving God, and inconsistent with his own commands?  Here, I would like to make the case for consistency and justness.

1. The nations of Canaan were evil, harming others, and needed to be stopped.  They had carried out incest with children/grandchildren and performed child sacrifice by fire. (Lev 18:6-30, Deut 12:31, Deut 18:9-10, Psalm 106:35, 37-38)  They launched unprovoked attacks on Israel (Ex 17:8-9, Num 21:1, Num 21:2-23, 33) and even guerrilla attacks against Israel’s “stragglers in the rear of the march when you were exhausted and tired.” (Deut 25:18)

2. Warfare language was likely rhetorical.  There are five reasons to support the rhetorical nature of languge such as “completely destroy” (Hebrew תחרימו, literally “ban”) in Deut 20:17.  It likely meant a destruction of armed soldiers, buildings, and religious icons.

1.  Semitic language professor and NIV, NAB, and ESV bible translator Richard Hess argues that Hebrew “ban” is “stereotypical for describing all the inhabitants of a town or region, without predisposing the reader to assume anything further about their ages or even their genders” and “need not require that there really were children, senior citizens, or women there who were put to death” even when followed by the terms “men and women” (Joshua 8:25) or “young and old” (Joshua 8:25).
2. In Israel’s destruction of enemies we see phrases like “left no survivor” and “utterly destroyed all who breathed” (Joshua 10:40, Judges 1:8).  But in Joshua 21:12-13 the author has no problem telling us these people were still there afterward: “if you ever turn away and make alliances with these nations that remain near you… God will no longer drive out these nations”.  In 1 Sam 15:3-4 Israel was to “strike down the Amalekites. Destroy everything that they have. Don’t spare them. Put them to death–man, woman, child, infant, ox, sheep, camel, and donkey alike.”  In 15:8 Saul “executed all Agag’s people” and Agag himself was killed in 15:33.  But later in  1 Sam 27:8 we’re told they’re still there and ” had been living in that land for a long time”.  Hundreds of years later in Esther 3:1 we’re even told Haman was an Agagite, a descendant of the Amalekite king Agag.
3. Most verses on the subject speak of “driving out” and “disposessing” the land rather than language suggestive of genocide.  E.g. Num 33:51-53, in “the land of Canaan, you must drive out all the inhabitants of the land before you. Destroy all their carved images, all their molten images,  and demolish their high places.  You must dispossess the inhabitants of the land and live in it, for I have given you the land to possess it.”  It’s the same story in Lev 18:25, Num 23:31-32, Deut 6:19, 9:4, 18:12, Joshua 3:10, and 23:9.
4. Jer 4:20 suggests inhabitants fled before armies arrived:  “At the sound of the horseman and bowman every city flees; They go into the thickets and climb among the rocks”
5. Deut 7:22 specifically says that Israel was forbidden to “destroy them all at once” and instead they would be expelled “little by little”.

So either all of these verses contradict one another, or the conquest language was rhetorical.

3. Many of the “cities” were probably military outposts.  For example with Jericho and Ai, Richard Hess argues there are no references to noncombatants (apart from Rahab), no archaeological evidence of non-millitary use, the term melek (Hebrew מלכי)  for “king” of the cities often meant mean a military leader in Canaan (e.g. in Joshua 2:2), they were located at defensive positions, and Jericho and Ai weren’t described as a large city as Gibeon and Hazor explicitly were.

4. A just God requires wrath.  It’s not possible to have a God who is just but not wrathful–otherwise wrongdoers continue unabated. Paranormal investigator James Randi wrote in Skeptic Magazine, “I accuse the Christian god of murder by allowing the Holocaust to take place” yet Dawkins and Hitchens condemn God for judgment against the Canaanites.  Which is it? Ultimately the the problem is we view death as the ultimate judgment, when in the theological context of the bible it’s only a graduation to what’s next with accountability for what we’ve done with what we were given.

The four points are developed with links for support. If you get this a question a lot, it’s a good resource to bookmark.