In Xcode 3, it was relatively easy to sort the source tree by name (see here for more details). However, I cannot figure out how to sort files and groups in Xcode 4 without manually dragging them.
There is no type of drag and drop for the project navigator. Probably because it would be too easy to erase your thorough organization.
Starting with Xcode 4.3.1 - select the folder / group in the project navigator area. Then go to Edit-> Sort, and you can choose "by name" or "by type."
To accomplish something like this without touching your proj file, you can become best friends with CMD-SHIFT-O (Open Quickly ... was CMD-SHIFT-D in Xcode3). Start typing the file name, and you will see a list of relevant files, and you simply select from the list.