If you edit es_systems.cfg via SSH:
nano /home/pi/.emulationstation/es_systems.cfg
Locate the emulator you wish to modify and change the runcommand.sh start type from 1 to 2. For example, in the Playstation section you need to change this line:
/home/pi/RetroPie/supplementary/runcommand/runcommand.sh 1
so it reads:
DESCNAME=Sony Playstation 1
NAME=psx
PATH=/home/pi/RetroPie/roms/psx
EXTENSION=.img .IMG .7z .7Z .pbp .PBP .bin .BIN
COMMAND=/home/pi/RetroPie/supplementary/runcommand/runcommand.sh 2 "/home/pi/RetroPie/emulators/RetroArch/installdir/bin/retroarch -L /home/pi/RetroPie/emulatorcores/pcsx_rearmed/libretro.so --config /home/pi/RetroPie/configs/all/retroarch.cfg --appendconfig /home/pi/RetroPie/configs/psx/retroarch.cfg %ROM%"
PLATFORMID=10
Then press ctrl-x and then y to save.
This should preserve the aspect ratio