The major problems with Collins' arguments are:
1) He presents a straw-man of ID. He obviously has never read any ID works.
2) He constantly assumes methodological naturalism to attack ID but does not apply MN to his own arguments for God's existence (such as the physical constants of the universe). [Also, MN has been dealt with in philosophical literature, and he completely ignores that as well.]
3) His Darwinism undercuts his argument for God's existence from aesthetics. According to Darwinism, the only reason why he believes in God is because natural selection has caused him to for survival purposes, not necessarily because it is true.
4) His belief in methodological naturalism undercuts his Christianity entirely as it would eliminate the Resurrection of Jesus as a possibility in favor of naturalistic options (no matter how implausible).
5) He uses the argument from 'Junk' DNA when, in reality, that argument has been debunked for a long time. 'Junk' DNA is fully functional. Other arguments are dealt with in Dembski and Wells' book mentioned by Steve above.