Packages that need to be included in a specific order
Freek Dijkstra has put together a nice wiki of Latex package conflicts. Hyperref is the one he singles out for criticism: it has the nasty property that sometimes it conflicts when it is put earlier, sometimes when it is put later than other widely used packages, encouraging cargo-cult document headers.
He's had less trouble with inputenc conflicts that others, judging from complaints that I've seen, mostly, I guess, because he uses Xetex.