When using Template Builder (eg: for debugging a template), running the template will fail with the error 'could not load file or assembly'.
This issue occurs even though the same template can be successfully rendered as a Preview within the Content Manager Explorer and all the dependencies are registered in the GAC and Tridion.ContentManager.config file.

Solution: Merge dependent assemblies with ILMerge

If Template Builder is throwing such exception despite having the assemblies in the GAC, the recommendation would be to use of ILMerge to make Template Building Blocks (TBBs) self-contained and prevent having to do additional, manual deployment actions on all Tridion Content Manager servers.

Here is an example of the procedure of combining the assemblies and including them in the post-build event of the project in Visual Studio, just before the TCMUploadAssembly.exe tool:
 

echo Performing ILMerge on output dll (including assembly1 and assembly2) "..\..\..\packages\ILMerge.3.0.41\tools\net452\ILMerge.exe" "$(TargetPath)" "$(TargetDir)assembly1.dll" "$(TargetDir)assembly2.dll" /out:"%TEMP%\$(TargetFileName)" /target:library /log echo Uploading dll and pdb to CMS "..\..\..\..\Tridion\TcmUploadAssembly.exe" /verbose /uploadpdb:true  /targeturl:https://<CMEURL>/ "%TEMP%\$(TargetFileName)"

Once done, Template Builder should be able to run successfully the template.