In This Article from Joel on Software, Joel talks about how the easiest parts of the screen to click are the edges, and how putting menu bars at the absolute top of the screen increases usability. Can this principle still be applied to web apps, even though you can get to the absolute top of the screen due to the browser, or is it a moot point?
I'm surprised the article doesn't mention Fitts' Law, which states that the bigger the target is, the easier it is to acquire. (That's only half of the law, but it's the part that interests us here.)
A menu bar may be considered infinitely large if it can be activated by clicking anywhere "above" the screen.
You should read A Quiz Designed to Give You Fitts, by Bruce "Tog" Tognazzini, the same person who wrote the article to which Joel alludes. The Macintosh pull-down menu is described in Question 5.
To answer your question, web pages can't use the edge of the screen as a Mac's menu does. So that's not a good reason to put a menu at the top of a web app. (Granted, there may be other good reasons…)
I think this principle is still valid, albeit the reasons have changed a bit.
Although you cannot "throw" the mouse and hit a corner, it's still easier to target something on the edge or in a corner as it has less neighboring elements:
Think of 3 buttons in a row - if they're small and you're trying to hit the middle one fast, you can err on both sides. However, if you approach the extreme ones (especially from their "neighborless" side), the chances of hitting another button are slim.
Besides, this has been the best practice of dialogs as well, which are not on the edge of the screen either.
The corner is not only more visible, but we've also grown accustomed to finding the "important" actions there.
On the second paragraph, Joel makes a comparison between the mac menu bar and window's one. It is noted that the "mile high menu bar" is the mac's as being attached to the border of the screen makes it infinitely reachable, as even throwing your mouse, you will always reach it. Window's solution does not benefit from this as you have to "point" to the bar since it is attached to a movable window.
Much like the windows bar, any web application embedded in a window lacks the "mile high" reach, unfortunately.