So I make drag these apps into nice grids: - a small left hand strip for Twitterific, iChat, Skype etc. this strip also pushes the next windows a bit more to the center. Helpful because the 30inch is so wide. - Safari, Texmate, Firefox etc. is next.My default Safari width is often the width of Apple.com so no scrollbars are shown. - leftover space is for PDF documentation and when I need 2 windows next to each other e.g. 2 Xcode windows. Plenty of space left for that.
Apps like Logic Pro, Aperture, iPhoto, iMovie, iTunes are run maximized/fullscreen.
Terminal.app is indeed ill-equipped when it comes to resizing etc. I usually build a couple of window groups that fit my needs (e.g. four-in-a-square with a wide window for logs) and open-and-close such a window group if the current layout isn't optimal.