I understand that sharepoint creates the SharePoint Web Services for a number of purposes, as described here.

Here is my particular instance:

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Is it possible to organize/rename these GUID named applications without breaking any useful behaviours they perform?

Furthermore, why are some of them named with GUIDs, whereare the topology and Security Token service application are given more friendly names? What gives?

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You should never change these GUID's as that will break your SharePoint farm. Those GUID's aren't pretty and are indeed implemented inconsistently, but we'll just have to live with them.

Making other changes to IIS settings should be done via SharePoint (GUI, PowerShell, Object Model) when possible. Only reside to making manual changes when know what you are doing. A typical example is changing the application pool identities in IIS. That might work for some time, but as soon as you make changes like adding another server, SharePoint will provision IIS with its original settings as it is unaware of your changes.

There are of course things that you will have to do in IIS, like adding SSL certificates. But again, check if there is a SharePoint way first.

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1) If you rename them, you will break SharePoint's Service Applications

2) The GUID ones are from Service Applications, of which Topology/Security Token Service are not.

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