As someone who worked for GeekSquad I can shine some light on any questions people have about Geek Squad practices and such. I will not give information out about specific partners since I no longer am employed with them and cannot confirm or deny who they all partner with.
The Diagnostic tool they use is a custom piece of software built on what I assume is a basic Linux disto/windows boot disc. When booted into this custom OS from either the Network/USB/CD (depending on the computer in questions capabilities or what is wrong with it) it will boot into this OS. From there it allows the agents to use many tools and software for troubleshooting. When I was there it had software for full hardware testing and multiple antivirus/antimalware tests. The antivirus/malware had multiple companies as it wanted to grab as much info as possible. You can run a complete scan allowing agents to plug in multiple machines in this virtual environment and it will send the logs to a central location where the techs can then look at this information.
Once they have more information they are decide what to do after. The reason for the diagnostic price is for multiple reasons.
1. GeekSquad is there to make money when you bring a car to a shop they can charge you to look at it the same way regardless if there is something wrong or not. You are in theory paying someone who is trained to look at you pc.
2. It stops everyone from rushing GeekSquad and people pushing "quick fixes" where something that can be fixed in 5min (hijacked webbrowsers I never charged for) this leads to people wanting more and more for free. So this allows them to put a wall up for that.
Note that not every GeekSquad has the same people so I can only communicate my experience and while I was there I tried to bring a professional and easy fix to all clients since GeekSquad doesn't always get the best reputation.