1. As an ecologist, I'm in total agreement with John Whitfield at Blogging the Origin when he says that reading Chapter III engenders the feeling that there's nothing new under the sun. An old joke in philosophy is that all philosophy is footnotes to Plato. After reading chapter III of the Origin, one could be forgiven for thinking that all ecology is footnotes to Darwin.
2. Chapter IV also has plenty of prescient bits, my personal favorite of which is the passage on p. 113 stating that it has been 'experimentally shown' that diverse mixed plots of grass will be more productive than plots sown with one species. The diversity-productivity relationship has been the subject of intensive recent research, and broadly speaking, Darwin turns out to have been right: more diverse plots are more productive. But the underlying mechanisms have been controversial (at least they were for a time). The main issue is/was how to distinguish between an effect of diversity per se on productivity from the effects of particular species (all else being equal, a more diverse plot is more likely to contain a dominant, highly-productive species). In my own work I've helped develop a solution to this issue. Interestingly, the solution is based on George Price's work on the mathematics of natural selection (see Fox 2005). Briefly, dominance of a mixed plot by a highly productive species turns out to be formally analogous to the increase in frequency of a trait favored by selection. We can use Price's mathematics to factor out this effect, leaving a remainder that isolates the effect of 'diversity' per se on productivity. So this little subfield of research has come full circle: Darwin raised the example of the diversity-productivity relationship because of its implications for his evolutionary ideas; it now turns out that Darwin's evolutionary ideas have implications for understanding the diversity-productivity relationship. Not sure how interesting this is to anyone besides me, but I assume if you've read this far you found it at least mildly interesting... ;-)
3. A historical note related to #2: Darwin doesn't cite the experiment to which he was referring, but my friend and former colleague Andy Hector recently identified it. It turns out to have been, as far as we know, the very first 'ecology' experiment ever conducted, predating Haeckel's coining of the term 'ecology' by several decades. See Hector and Hooper 2002 Science 295:639-640 for this interesting historical nugget.
4. Given Darwin's prescience in so many areas, I was a little disappointed to see that his theory of the origin of species relies so heavily on the principle of divergence of character (i.e. you'll be fitter if your offspring are more variable). It certainly wouldn't have been beyond Darwin to have thought up more modern ideas, such as that widespread species often comprise geographically-separated subpopulations living in different environments and therefore subject to different selection pressures, which will drive them apart in the long run as long as rates of gene flow among subpopulations are sufficiently low. I was expecting to see a clear statement of this idea, and I never did. EDIT: whoops, Darwin does indeed hit on this idea. On pp. 107-108 he refers to subsidence converting a continent into large islands, thereby isolating separate populations of the same species. And then he says "...after physical change of any kind, immigration will be prevented, so that new places in the polity of each island will have to be filled up by modifications of the old inhabitants; and time will be allowed for the varieties in each to become modified and perfected." And of course, this passage is a summary of what has come before. I suppose I missed it because Darwin often intermingles this idea with other distinct but related ideas (e.g., on p. 103, when he talks about the spatial scales on which we should expect to see variation within highly-mobile species like birds vs. less-mobile species).
5. The later parts of chapter IV (pp. 116-130), on the 'tree of life' and the problem of classification, was interesting to me as proposing a solution to a problem that, as modern readers, we don't even recognize as a problem. The Linnean system of classification is hierarchical: species are nested within genera, which are nested within families, etc. What justifies (or maybe better, 'motivates') a hierarchical classification system? After all, there are many non-hierarchical possibilities. One could, for instance, group organisms into 'functional groups' based on their ecological 'roles' (e.g., herbivores, carnivores), and these groups would not be hierarchical but rather overlapping (e.g., some organisms are both herbivorous and carnivorous). I'm sure that various non-hierarchical classifications schemes were proposed at some point in the history of science (anyone know anything about this?). But if all life really does comprise a single branching evolutionary 'tree', that's a strong motivation for choosing a hierarchical classification system which reflects the hierarchical nature of 'tree-like' branching. This gets to philosophical issues regarding 'natural kinds'. Nature is full of variable 'things' that are similar in some respects and different in others. Is there ever a 'natural' way to classify these things, to 'cleave Nature at the joints'? Or is classification merely a human construct, something we do strictly for our own convenience?