I've found Programming Windows to still be useful. Thanks to Microsoft's emphasis on backwards compatibility, all of the core stuff (window handles, messages, GDI, etc.) seems to still be relevant and is covered well in Petzold. (If anything changed too drastically, it would break too many existing Windows programs, and the huge number of existing Windows programs is a big part of Windows' advantage in the marketplace.)
There are specific new APIs, like Setup API, the Thread Pool API, and GDI+, and there are new topics such as working within the context of Vista's and 7's UAC. There are also several individual new functions, that Petzold doesn't cover, but it's easy enough to look up newer topics on MSDN as needed. Programming Windows also doesn't cover COM, which can be a big part of Windows programming.
Keep in mind that the API that Petzold covers is all low-level and C-based. (There are a few newer APIs, like GDI+ and some of the COM stuff, that are object-oriented.) Virtually any modern development will be object-oriented and will often use a framework like .NET or Qt or Delphi's VCL, so you'll rarely write complete applications that look like the example code in Programming Windows; however, it's still great for explaining what's going on under the hood.
I looked around a while ago and couldn't find any newer API references. I suspect this is because of the sheer size of the current Windows APIs; Programming Windows, 5th Edition is already almost 1500 pages long, a book that covered anything new would be too huge. I did find a couple of interesting-looking supplements to Programming Windows, although I haven't read them yet:
- Essential COM, by Don Box - Several of Vista's new APIs are COM-based, and Petzold doesn't cover COM.
- Windows System Programming, by Johnson M. Hart - seems to entirely skip the GUI and GDI stuff that Petzold covers so well, but it has much more detail on modern approaches top multithreading, IPC, etc.
- Windows Internals, by Russonovich, Solomon, and Ionescu - less about APIs and more about how Windows works under the hood. Russonovich possibly knows more about this than anyone inside or outside of Microsoft.