"For my thoughts are not your thoughts..." Isaiah 55:8

There are a lot of verses in the Bible that people quote without really understanding whether or not they apply to the situation at hand.  Christians often quote Isaiah's words about the will of God when talking about tragic situations like cancer, a house fire, a hurricane, or simply some loss or failure that doesn't make any sense to us.  In that vein, this verse is much like Romans 8:28-29, a verse that when taken out of context doesn't necessary lead us into error, per se, but certainly takes us away from the point that the writer, and thus God, are trying to make.
In Isaiah 55, God is expressing his willingness to not only save and restore Israel after the upcoming judgment falls upon them, but surprisingly he plans to include the nations that haven't even heard his name yet in his redemption.  In verses 6-7 God explains that he is near and easily found by anyone who is willing to repent by turning from their wickedness.  It is at this moment that God says, "my thoughts are not your thoughts, neither are your ways my ways."  He certainly isn't talking about understanding or coping with tragedy or misfortune, but instead about how God's love and mercy for sinners is beyond our understanding.
The people of God have a long running tendency to exclude those they don't like or aren't comfortable with from the reach of God's mercy.  This began with the people of Israel and continue in the history of the Church.  From Moses to Jesus it was the Jews who were reluctant to extend God's grace to the Gentiles, once the Gentiles took over the Church they turned the tables and ensured that the Jews were no longer welcome, and later on added in other undesirable such as the American Indians, African slaves, and other groups.  It took generations of dedicated work by missionaries and reformers to fight back against this latent racism, to purge the Church of a willingness to forget about those who had not yet been given a chance to accept the call of God to repent.
This same line of reasoning applies to God's willingness to forgive repentant sinners that have either fallen too far in our view, or who have committed sins that we find more repugnant than the ones we've been guilty of.  At times this manifests itself in a reluctance to forgive those whose crimes against God seem somehow more grave than our own, at other times it shows up as a reluctance to allow our social club feeling of Church to be distracted by the likes of such sinners as drunkards, drug users, prostitutes, gamblers, or those with sexual perversions.  Are the sins of vanity, greed, or good ol' heterosexual fornication somehow a better class of sin?  Are those who have already received God's forgiveness somehow superior to those who are about to?
Why are God's "thoughts" and "ways" not our own?  Because we have not yet allowed the transforming power of the Holy Spirit to eradicate the self-righteousness from our own thoughts and attitudes to the extent that we  begin to see what God see when he looks upon a Lost sinner, a child of God who needs to come home.  That God's "thoughts" and "ways" are not our own is a good thing, a merciful, loving thing, thanks be to God.