Basically, somehow my ~/.local/share/applications/opera.desktop file got messed up:

[Desktop Entry]
Encoding=UTF-8
Version=1.0
Type=Application
Name=(72) Facebook - Opera
Icon=opera
Exec=/usr/lib/x86_64-linux-gnu/opera/opera
StartupNotify=false
StartupWMClass=Opera
OnlyShowIn=Unity;
X-UnityGenerated=true
MimeType=x-scheme-handler/unknown;x-scheme-handler/about;x-scheme-handler/https;x-scheme-handler/http;text/html;

Adding %U to the end of the Exec= line fixed it. (And, of course, I got rid of "(72) Facebook - " in the Name= line. How the heck did this happen??? Dunno, but this is how to fix it in case anyone else has this problem. Man, I tolerated this problem for MONTHS! Glad it's finally fixed.

Any help?

If the problem is in this script, though, wouldn't this be a widespread problem? I'd think something like that would have been reported and fixed already. Regardless, it'd be good to investigate this angle, so I'm wondering if you could post your script or suggest any changes to mine?

My Opera bash-completion script:

# opera(1) completion                                      -*- shell-script -*-

_opera()
{
    local cur prev words cword
    _init_completion || return

    case "$prev" in
        ?(-)-widget|?(-)-urllist|?(-)-uiparserlog|?(-)-uiwidgetsparserlog|\
        ?(-)-profilinglog)
            _filedir
            return
            ;;
        ?(-)-[psb]d)
            _filedir -d
            return
            ;;
        ?(-)-remote)
            COMPREPLY=( $( compgen -W 'openURL\\( openFile\\( openM2\\(
                openComposer\\( addBookmark\\( raise\\(\\) lower\\(\\)' \
                -- "$cur" ) )
            [[ $COMPREPLY == *\( ]] && compopt -o nospace
            return
            ;;
        ?(-)-windowname)
            COMPREPLY=( $( compgen -W 'first last opera{1..9}' -- "$cur" ) )
            return
            ;;
        ?(-)-geometry|?(-)-window|?(-)-display|?(-)-urllistloadtimeout|\
        ?(-)-delaycustomizations|?(-)-dialogtest|?(-)-inidialogtest|\
        ?(-)-gputest)
            # argument required but no completions available
            return
            ;;
    esac

    if [[ "$cur" == -* ]]; then
        COMPREPLY=( $( compgen -W '$( _parse_help "$1" -help )' -- "$cur" ) )
        [[ $COMPREPLY == *= ]] && compopt -o nospace
        return
    fi

    _filedir '@(?([xX]|[sS])[hH][tT][mM]?([lL]))'
} && complete -F _opera opera

# ex: ts=4 sw=4 et filetype=sh

I run the Developer version and thus can't tell you what the stable version has in its script at this point. The Developer version works properly when I click a link in my email, so I'll assume it's an error in the script as described - unless it's a setting in your email software as to what program is called and how. But as you said it also happens from a terminal, I guess we can exclude the email program.