It's frustrating the way the colour balance shifts - silly automatic camera
As I recall (and it's a while since I last used it) Hugin does allow you to tell it to compensate for things like Brightness variations (somewhere near the end, when it does the proper stitching bit).
I used to find it easier to generate multiple TIFs and then combine them with enblend, which did a much better job than Hugin of joining, and smoothing the edges. I think that Hugin has improved this a lot in the more recent variations, but it might be worth trying enblend if you're still having problems (it is a command line program, but it's not that difficult to use).
yes, hugin can set the brightness variation. i'm using the mac osx version - it's on the first screen when you add the photos. you select the photo that has the exposure you want to use for the rest of the series and click "Anchor this image for exposure".
also, the version of hugin i'm using 0.6.1 (i think this is quite old, i installed it a while ago, but i've only been using it recently) gives the option of using enblend when you set the output filetype to be tiff.
That wave... did you stitch together multiple waves?
No it's just cropped to make the letter box shape. I suppose you could say it's cheating, but I like the result.
I have been playing with Hugin, and so far I'm pretty impressed. I've played with a few stitching programs and Hugin is the best yet. A couple of early results...
as far as i'm concerned it's the aspect ratio of the final image.
looks like i picked the best to start with (hugin is the only pano app i've used).