Hey, can I ask a favor? I want to apply this, but before I do, I need to make absolutely sure that this works in:

1. IE 6 (which supports only the filter syntax)
2. IE 7–9 (which support both filter and standard CSS opacity)
3. IE 10 (which supports opacity but removes support for filter)

If you can assure me that the tests pass in all three of the above (for #2, testing any one of IE 7, 8, or 9 works for me), then I'll merge this. I'm very cautious about this code because I last touched it to add support for IE 10, and it was painstaking surgery to arrive at something that worked everywhere.

1. I've ran Prototype opacity unit tests (in dom_test.html) in IE Tester (IE6, 7, 8, 9), and in standalone IE7, IE8, IE9, IE10 (on different PCs), and also in recent versions of Chrome, Firefox, Opera - OK (to be absolutely correct, I've got some test failures, e.g. in testGetElementsByClassName in IE6-7-8, testElementScrollTo in Chrome and Firefox, testElementSetStyle in Opera, testToQueryString in all browsers, many of selector_test.html in IEs, but those tests are not relevant to the subject).
2. I've ran Scriptaculous unit and functional tests in the abovementioned browsers. Opacity in effects and draggables works fine (well, almost fine - all IEs including IE10 have smoothness/performance problems).
3. I am using this code in production (24x7 cross-browser intranet web app) since at least 28.06.2012. Strictly speaking, I've started this code after profiling my app in IE8-9, then used it for a while in production, and only now made pull request.

There is another opacity-related issue, now in Opera: https://prototype.lighthouseapp.com/projects/8886/tickets/1282-latest-prototypejs-from-github-repo-fails-in-opera - should I make another pull request or include in this one?

I'd say make another one. I'll merge this one soon enough.