list graphical processes from terminal

Try xrestop or xrestop -b.

It is intended to measure how many X resources each X window consumes, but as a small bonus identifies name of the windows and corresponding PIDs.

xlsclients is close (and a standard part of X), it lists the X server's clients. But, there might not be a 1:1 mapping between what you consider an "application" and what X considers a "client". My single running instance of LyX consumes 13 clients for example, if I use xlsclients -l (long-form output) I can see only one of them has a defined "Icon Name", but this is only a hint. Also, since it uses XQueryTree() it may miss some windows (it doesn't find any xpdf windows I have open).

It also doesn't give very much information, what you can do though is use xlsclients -l to obtain the window id, and query each window with xprop -id $ID. For more details on a window, use xwinifo, though it cares about "windows" which are not the same thing as clients or applications:

xwininfo -root -children
xwininfo -root -tree  # indented view

Depending on your window manager, you may be able to inspect certain window properties (e.g. _NET_xxx or _NET_WM_xxxx properties) to determine if something is an "application". If the window manager client or GUI library sets it (any contemporary one should) the _NET_WM_PID property is the simplest (though imperfect) way to associate a PID with a specific window. I don't know of a tool that ties all these pieces together.

I use the window manager FVWM, I can talk directly to it using FvwmCommand, e.g. FvwmCommand -i1 send_windowlist shows me the list of windows. @Arkadiusz' suggestion to use wmctrl seems like a good and window manager agnostic way to do the same thing.

One more trick is to query the root window's _WIN_CLIENT_LIST, via bash:

$ xwininfo -root 
xwininfo: Window id: 0x69 (the root window) (has no name)
[..]

$ IFS=",= " read -a win < <(xprop -notype -id 0x69 32x  _WIN_CLIENT_LIST )

$ for ((ww=1; ww<${#win[*]}; ww++)); do 
    printf "%i %s\n" $ww ${win[$ww]};  
    xprop -id ${win[ww]} -notype _NET_WM_PID WM_NAME WM_CLASS \
                                 WM_ICON_NAME WM_CLIENT_LEADER; 
  done

This exactly matches what my WM lists as windows (without those I have configured to be excluded from the WM window list). Child windows set WM_CLIENT_LEADER to their parent (for session management), though the parent window may not be visible (firefox does this), and may point to itself.

xrestop gets my vote though.

Alternatively, if you're using EWMH compatible window manager you can give wmctrl a try. It can list all windows being managed by the window manager + their PIDs:

$ wmctrl  -lp | awk  '{ print $3 }' | sort | uniq
15672
19685
19925
26247
6884