Depends on what "evolution" is taken to mean. There's 'evolution' in the sense of
change over time, there's 'evolution' in the sense of
natural selection, there's questions about the
pace and rhythm of evolutionary change (saltationism and punctuated equilibrium), there's ecological and population approaches and cladistic and genomic approaches, there are all kinds of controversies revolving around the hugely complex problems of reconstructing phylogenies, the problem of how much of evolutionary theory is really based on empirical observation and how much is armchair philosophizing, questions of precisely what is being selected by natural selection, problems of taxonomic classification, and many many more.
Here's a short little account of the 20th century developments in phylogenetics written by an outspoken proponent of Hennigian cladistics from the U. California.
http://ib.berkeley.edu/courses/ib200/readings/Mishler 2009 (Taxon).pdf
There are probably questions about and arguments raised about just about every aspect of evolution with a whole variety of views proposed. What looks to the layman like (and is often presented to the layman as if it were) a simple open-and-shut case gets tremendously complicated and even controversial when seen from a professional point of view. That's what evolutionary biologists spend much of their time arguing about in the journals.
But I take it what isn't what this thread is about. You aren't asking about controversies
within evolutionary biology (which may result in much of it being questioned at one time or another in that context, where phylogenetic change-over-time and natural selection are pretty much givens) but about criticism of evolutionary biology from
outside, intended to question and to refute exactly those fundamental ideas. You many or may not (I don't want to put words in your mouth) be inquiring into what the best arguments are for "ID".
My own view is that the best argument for "ID" is probably Behe's Irreducible Complexity argument:
"This creates a problem for the Darwinian mechanism. Natural selection preserves or "selects" functional advantages. If a random mutation helps an organism survive, it can be preserved and passed on to the next generation. Yet, the flagellar motor has no function until after all of its 30 parts have been assembled. The 29 and 28-part versions of this motor do not work. Thus, natural selection can "select" or preserve the motor once it has arisen as a functioning whole, but it can do nothing to help build the motor in the first place."
The idea is that many biological systems are exactly that,
systems. They are combinations of elements, sometimes quite complex combinations, that together perform a function. The completed function might obviously be advantageous to the organism and thus subject to natural selection, but none of the individual elements of the system possess that selective advantage. So what explains the original origin of the system?
Before Sciforums has collective apoplexy and starts flaming me, I'm not persuaded that this problem is anywhere near a slam-dunk disproof of evolution. But it is an interesting conundrum.