Ubuntu – How to set default encoding for non UTF encoded documents system wide

iconv is probably what you'll want to use. iconv -l will show you the available encodings and then you can use a couple of commands to recode them all:

# all text files are in ./originals/
# new files will be written to ./newversions/

mkdir -p newversions
cd originals
for file in *.txt; do
    cat $file | iconv -f ASCII -t utf-8 > ../newversions/$file;
done

If you want to do this with files you don't the encoding of (because they're all over the place), you want to bring in a few more commands: find, file, awk and sed. The last two are just there to process the output of file.

for file in find . -type f -exec file --mime {} \; | grep "ascii" | awk '{print $1}' | sed s/.$//; do
    ...

I've no idea if this actually works so I certainly wouldn't run it from anything but the least important directory you have (make a testing folder with some known ASCII files in). The syntax of find might preclude it from being within a for loop. I'd hope that somebody else with more bash experience could jump in there and sort it out so it does the right thing.

As of the time of this writing, It seems that gedit does not officially expose the character encoding used to decode an open document.

Gedit does show some encoding in the Save As dialog window. It is likely that this is the encoding that was used to decode the original file. However, without inspecting the source code of your version of gedit, there is no guarantee that the encoding shown is the actual encoding used.

Muru has indicated (above in the comments section) that gedit exposes encoding information to plugins. I have yet to come across a plugin that adds this information to the gedit's user interface.