Prod and wait
I don't like to post a somewhat serious response to a fun article but as a recovering Windows support tech who has read lots of packet sniff collections of MS network cruft, I can't stand to see someone experiencing the prod and wait phenomenon without sharing some common causes.
Some common causes are:
1. MS Outlook - No surprise there, but MS Outlook is a network pig that insists on sending out a horrible number of "are you still there" minimum size packets to the MS Exchange server. If the MS Exchanger server is slow or is accessed over a WAN link, then MS Outlook will slow down the entire OS. Easiest way to fix is turn on the "Connect to my Exchange mailbox using HTTP" option. It is a much more sane way for Outlook to jabber at the Exchange server.
2. Shortcuts to files on servers on the other side of a WAN link - If you are the kind of person with shortcuts littered throughout the desktop and start menu, this will slow down the entire OS because almost every time you ask the OS to do something, it will send out 'are you there' minimum sized packets to all the servers where you have shortcuts before it does what you want it do. Seems insane, but there you have it. Best way to fix it is to not have shortcuts that point to servers that are not on your LAN.
3. Shortcuts to files that don't exist - See point 2 but multiply the effect by about 10 because the file is not there, which means more jabbering (are you really, really, really not there?). The fix is to clean up your shortcuts.
4. Some turd decided to redirect your 'My Documents' to a file server that is on the other side of a WAN - See point 2 but now add in even more 'are you there' packets because the one folder the OS must see is on the other side of WAN link. This is hard to fix because 9 times out of 10, a MS drone has set this configuration up centrally and is managing your desktop :p
These problems are common in business networks where servers have been consolidated into a couple of data centers (who knows where) but the MS drones have not consulted the network folks on the impact of latency introduced by *all* WAN links on the OS's that are used. The fact is, Windows is set up for LAN latencies and even an extra 5 ms of latency causes the Windows OS's to pause when poked. It can't be fixed by buying more bandwidth. It is a function of latency. Try searching the interweb for Big Fat Pipes if you want an eye opener on the subject.
MS Windows can be modified somewhat via the registry to reduce the impact of latency higher than LAN latency, but for that, you must do more research (and not be locked out of it by the MS drones).