MikTex and Gnu Emacs

Short answer: yes for EMACS (I don't know the other app)
If you put the EMACS directory under PortableApps, the remaining issue is that EMACS doesn't have an executable in the main directory. It is located in the 'bin' sub-directory. So, you need a batch file like this in the main directory:

echo off
cd bin
emacs.exe %2 %3 %4 %5 %6 %7 %8 %9

If you use one of the PAM variants or other menu programs that can pick up BAT files, you're done (do follow your menu program directions to add a menu item to this batch file).

If you are using the current official release of PAM, you have one more step; use one of the BAT-To-EXE converters (discussed in these fora) to convert this batch file to an exe file in the main EMACS directory. When you restart PAM, it will pick up the new exe file.