While I'm hardly an expert in paleontology, genetics, or molecular biology, I find a few strands of evidence almost irrefutably tip the scales in favor of evolution: vestiges of common ancestors that show up in leftover traits, atavisms, and pseudogenes. (I'll let you take the time to look these up, if you wish. Jerry Coyne's admittedly biased book Why Evolution Is True is a good place to start.) But I don't think ID and evolution are totally irreconcilable. Michael Behe, William Dembski, and Stuart Pullen have done much thoughtful research about the mathematical probablities involved in constructing useful molecular knowledge and complex systems which would seem to have no adaptive vantage apart from near-instantaneus development. This would seem to favor ID.* But given theism, it should be no shock or surprise simply to say that everything that has ever occurred in the universe's history has been by God's design and involvement. Christian theists don't need to argue or look for special evidences of "intelligent design" because the Bible repeatedly affirms God's providential hand in every single event in history, even those which may appear to us as "random" or purposeless.
Wayne Grudem provides a helpful definition of this providence in his Systematic Theology:
God is continually involved with all created things in such a way that he (1) keeps them existing and maintaining the properties with which he created them; (2) cooperates with created things in every action, directing their distinctive properties to cause them to act as they do; and (3) directs them to fulfill his purposes. (p. 315)
Let's examine each of these briefly (I'm largely following Grudem here):
(1) God upholds and maintains all that he created. We see this in Scripture in Jesus' active sustaining of the universe (Col. 1:17; Heb. 1:3), in God's preservation of the cosmos (Neh. 9:6; 2 Pet. 3:7, 10-12), in Paul's speech at the Areopagus (Acts 17:28), and in death as a result of God withdrawing his Spirit (Job 34:14-15; Ps. 104:29). Similarly, the properties of the world continue as they do in an act of God's grace upon sinners so that we can live in a reliable, predictable world (e.g., Gen. 8:22; Jer. 31: 35-36; 33:20-26). Consequently, whatever is happening in the natural world today can be assumed to have always been happening. Atoms will always behave as atoms do; erosion keeps eroding; matter always warps space-time; entropy of closed systems always increases; etc.
(2) God cooperates with created things and directs their endowed properties so that they act as they do. Scripture says that God brings about all weather phenomena on Earth and even the movements of heavenly bodies (Job 37:6-13; 38:22-30; Ps. 104:4; 135:7; 148:8; Jer. 31:35; Matt. 5:45). When animals eat, they are said to be fed by God (Job 38:39-41; Ps. 104:27-29; Matt. 6:26). Flowering is caused by God (Matt. 6:28-30). All of these may have "natural" or "scientific" explanations based on properties of matter and energy apart from any reference to God. But Scripture affirms that these properties were endowed by God and are directed by him, so that whatever happens in nature is an "act of God." (I hope insurance companies aren't reading this.) In a similar vein, even "random" events are attributed to God. "The lot is cast into the lap, but its every decision is from the LORD" (Prov. 16:33).
(3) God works purposefully in providence. Ephesians 1:11-12 says that God "works out everything in conformity with the purpose of his will . . . for the praise of his glory." God's will is that ultimately through the church and through the subjection of all things to his Son Jesus Christ, the Father will be glorified (Eph. 3:10; Phil. 2:10-11).
So perhaps we can summarize the biblical data with Calvin's famous maxim: "The will of God is the necessity of all things." In other words, if anything has happened, it has happened because God wanted it to happen at that time, in that way, for the sake of his wise goals. It didn't happen by itself; it was dependent upon God. It didn't happen haphazardly, randomly, or accidentally (though it may appear so to us); it was purposeful. The unveiling of that purpose might await, however, the final judgment and renewal of all things. It is not necessarily for us to know now (Deut. 29:29).
This view of God's sovereignty is a much higher view, in my opinion, than to say that God only acts or shows up in the "miraculous." In this latter schema, if something is truly an act of God, then it cannot have any human or natural explanation. Rather than exalting God's power, I think this view actually reduces God from being actively, caringly, and judgingly involved with every moment of everything to a semi-deistic God who only intervenes in his world here or there, like the Greco-Roman pantheon. The biblical view of God's action, however, can be seen in passages such as Acts 2:23: "This man [Jesus] was handed over to you by God's set purpose and foreknowledge;"--though to the common observer he was handed over by Judas Iscariot and the Sanhedrin--"and you, with the help of wicked men, put him to death by nailing him to a cross." Wicked men put Jesus to death, but yet it was also "by God's set purpose" and by Jesus' own will (John 10:17-18). Likewise, later in Acts we read that when the people conspired against Jesus, by their own volitional actions they "did what [God's] power and will had decided beforehand should happen" (4:28). God's planned action (primary causes) works through the agency of his creatures, through the abilities and properties with which they were endowed (secondary causes).
So what does this have to do with evolution? Everything. It means that we don't have to run from evolution when much evidence seems to confirm it (though some phenomena are still incongruent with it). We can instead view evolution and other natural phenomena as a window into the grand design of God. Yes, evolution is God's unfolding design in action. Behe, Dembski, et al., might be right: evolution in many ways may be mathematically impossible. But "all things are possible with God" (Mark 10:27). And even if it's found that such mathematical leaps aren't indeed necessary, then we can still rest in the knowledge that just as rains and seasons and nightfall are both naturally-caused and God-caused, so too is life on planet Earth. Accordingly, then, in opposition to evolutionary atheists, evolution does not mean that life is meaningless. Rather, life is incredibly meaningful. We have each been put in our time and place, with the world around us as it is, specifically as the stage for our humanity to be worked out, along with our own participation in the salvation and redemption of the world as we know it.
*As I see it, there is one flaw with these approaches toward calculting the probability of a given gene (and its resultant protein) being assembled. ID folks assume that if there is no known beneficial purpose for protein, then that entire gene could not have been preserved within the genome. Therefore if the protein exists, its gene--all hundreds or thousands of its DNA nucleotides--must have arisen all at once. But that's not necessarily true, and the likelihood of proteins arising stepwise by modifications of preexisting amino acid sequences greatly enhances their probability.