Depending on the manual you are looking for. The main reason everyone was wearing black in Winforms was less because the Microsoft manual stated that it should be (it is not), and more, because it was the default, and it hurt to write it differently. Even now, I would suggest that most LOB applications written using Silverlight or WPF will use the default colors and styles for the same reasons.
But many other user interface recommendations may apply. If you want to look and feel familiar, there is no reason why you cannot create a standard menu bar with files, Edit, View, Help, etc. You can still use the same keyboard shortcuts, the same commands, the same layout for buttons and controls.
Keep in mind that these recommendations were written with assumptions about software and computers in general that are no longer true. The dominant paradigm has changed, and people are much more used to sites with different user interface layouts and richer visual effects. As a result, the visual style is much more diverse, and people are less likely to be confused by some non-standard layouts and controls. This does not mean that something is happening, we just need to feel less restrained in order to keep things in the same order and position so that our customers do not worry, because they cannot find the save button.
In short, the style guide was there because it wasn't enough for a real designer, but still enough for developers to make things ugly. Now it’s even easier to do really ugly things, but there’s a lot that a real designer can do to make him enjoyable. So hire one. It's worth it.