Will fitlet run off-the-shelf, common apps under Windows 7 and Linux? I read in a few places that Linux on Media boxes could leave users very disappointed, even if they get the desktop environ up, because of the few apps that run on SoCs

fitlet is a VERY standard PC in that respect. All Windows and Linux applications should be 100% compatible.

Where are the "gotcha's" with other small systems?
Architecture (mostly ARM) - fitlet is AMD x86.
Non-standard BIOS - fitlet has AMI BIOS with both UEFI and legacy support.
Insufficient RAM - fitlet supports up to 8 gb
Insufficient storage / no SATA - fitlet has mSATA up to 1 TB or so.
Limited graphics, no DirectX / openGL - this was in fact a limitation with fit-PC2, but fitlet has Radeon built-in.

Bottom line - performance might not always be high, but compatibility is perfect.

Intel I218V and Intel I211-AT driver solution for Windows Server 2012 R2

I218 and I211 Ethernet controllers (adapter) used extensively in Compulab products for LAN communication. It's appears to be a common problem with this network adapters to operate them with server versions of Windows, due to Intel drivers settings. This post solves problem with Server 2012 R2, but it can be used for other versions of Windows Server i.e 2008, 2008 R2, 2012 and 2016.

Please note this solution hasn't been tested by Compulab.

Does FreeBSD run on fitlet?

FreeBSD works on fitlet in command line mode. Graphics is not supported.

Does fitlet support pfSense?

pfSense works well on fitlet.

Does fitlet support IPFire?

IPFire works well on fitlet.

Does fitlet support VMWare ESXi

ESXi is reported to work on fitlet, however a known issue with I211 NIC driver in ESXi software exist and addressed in few articles:

Note: The issue appeared on both ESXi 5.5 and 6.0 (VMware-VMvisor-Installer-5.5.0.update02-2068190.x86_64.iso).

What are the supported boot modes?

Both UEFI and Legacy boot modes are supported.

How can I monitor CPU temperature in Linux?

See Getting fitlet CPU temperature in Linux

Using fitlet GPIOs under Python

Refer to Forum example shared by DaveLangstaff.
fitlet GPIO SDK information can be found here in Fitlet GPIO Connector User Guide