PE-Bear allows you to specify a file to load from a prompt. Specifying more than one file only opens the first specified:

% PE-bear one.exe
% PE-bear one.exe two.exe three.exe    #### Only loads one.exe

Multiple files can be subsequently opened using File->Load PE or Control+O, but this dialog also appears to support loading one file at a time, which can become tedious when working with sets of files.

Please consider adding functionality to load multiple files at the same time.

If it helps, this is the version I am using:

PE-bear - Portable Executable reversing tool
version: 0.5.4 Qt5
built on: May 24 2021