This has been a minor annoyance for the last few months, and I've finally figured out how to fix it:
Sometime within the last few months, an upgrade prevented Chromium from finding its application icon…with the result that when minimised (or displayed in the panel window list or Alt-Tab) it used the default application icon.
It looks to me as if the problem is that Chromium is now looking for chromium-browser.svg but chromium.svg is what's on my debian system.
To restore, all you need to do is:
$ mkdir -p ~/.local/share/icons/hicolor/scalable/apps $ cd ~/.local/share/icons/hicolor/scalable/apps $ ln -s /usr/share/icons/hicolor/scalable/apps/chromium.svg chromium-browser.svg
great, done. Now my chromium windows don't look the same as my mrxvt windows in Alt-Tab, they're quite clearly Chromium windows. The icon now looks like this: 
rather than an icon i'd insert here if i knew what its filename is – it looks like a white window with a blue title bar and a thinner blue bar at the bottom (about half the height/thickness of the "title bar") I've spent half an hour searching for it and have given up – anyone know what it is?
alternatively, use cp rather than ln – just in case some future upgrade removes or renames the chromium.svg file