I agree with Keble, that using Thomism is usually not a good approach. I'm not saying the arguments of Thomas Aquinas are unworthy, simply that they require all sorts of assumptions to be taken for granted (and they are not taken for granted by most modern people.)
Modern westerners are an extremely cynical (not simply skeptical) and (perhaps most significantly) subjectivist bunch. Thus, like it or not, some attempt has to be made at meeting people on their own turf.
Another important consideration, is to not have false expectations of what apologetics are supposed to do. There is no such thing as a man convincing another man, intellectually, into becoming a Christian. Conversion is always something ultimatly between God and the individual. Apologetics should always be viewed as a means of breaking down obsticals which sin and the devil have devised to prevent people from opening their hearts. I am convinced that even if a hard core atheist is not entirely convinced argumentatively, it is still possible for them to be transformed, simply by their opening their heart for a moment (then, with time, everything else will sort itself out.)
In short, apologetics should shake an atheist out of their smugness for long enough that they may consider humility, and allow Christ to step through the door of their heart; for He is the light which the darkness cannot overcome, and I have no doubt that if they let Him put a foot through the door, He will do things to and for them that we are simply not capable of (and it is arrogant for us to think otherwise.)
As for which arguments to take, I think a good starting point is to have an atheist/agnostic to try to come to some understanding of just who he is as a human being. I'm particularly fond of Descartes arguments, which demonstrate quite clearly that we as individuals are not simply flesh robots, and if anything, the spiritual is far more immediate (and demonstrably real) than many of the things we take for granted. In short, from a subjectivistic p.o.v., I can have far more certainty that I exist (and that this existance is not purely material) than I can have that anything I experience via the senses exists (which completely undermines materialist assumptions about the world and the nature of our existance.)
Another fruitful argument along the same vein, is the one put forward by the Anglican bishop George Berkeley (1685-1753) who attacked materialism by undermining it's central dogma - the whole notion of their being actual material or physical objects. This argument does not mean that we do not believe in creation - only that the certainty of it is far, far less, than certainty regarding our own existance as spiritual beings.
Both Descartes' and Berkeley's arguments are very strong, and the counter-arguments against them are very weak (and can easily be routed).
Once faith in materialism has been shaken, and the objective existance of the soul (at least that of the atheist himself) has been affirmed, then a whole world of new possibilities is open for the cynic. Once again, arguments are not ends in themselves; but they can be important in shaking a secularist's confidence in the dogmas of his own godless faith (and there is most certainly a great deal of faith involved in materialist assumptions.)