Thanks, all.
[Hikaro] Compliments from veteran creators are especially encouraging. The thunderstorm took an enormously long time to do (although it wasn't nearly so bad as the cloak). Basically, I looked on the internet for a cloud animation, and it was surprisingly hard to find one. I don't have the link any more for the site where I got this one, but it had a number of computer-generated animations. I downloaded one and opened it up in Adobe Premiere, where I exported about twenty frames. Then I used NeoPaint to turn them all black and white, and also to create templates based upon them for the transparency. Then I basically treated them the same way as Kinboat's smoke animation - created a number of square primitives, mapped each frame onto one of them, parented them to an invisible ball, and displayed them in sequence throughout the animation.
The lightning is simply images mapped onto square primitives. In retrospect, the whole effect isn't really as impressive as I'd hoped when I conceived it, but I did want to do a lightning effect that was a little different from others that have been made. I got the idea of a cloud appearing and vanishing again from Populous II! I had to do quite a lot of postwork on the final storyboard to clean it up. In particular, the parts where the cloud appears and disappears - which looked great in the initial renders - went very pixellated once it was converted to 256 colours with a Civ-friendly palette. It still looks a bit pixellated even now, after I went through it manually smoothing it. I've found that transparency effects have a tendency to look rather clunky in-game, which is a shame.
Anyway, feel free to run the animations through Flicster and cut 'n' paste the spell effect out, if you so desire.