When I try to search for this problem I get many results, but most of them seem to be about mouse cursor themes, and I haven't played with that, and can't see how that could explain the symptoms I see.
When the mouse cursor is over a window from thunderbird, firefox or a (group) chat from pidgin, the mouse cursor is 2-4 times the usual size, that it has when over windows with xterm, liferea, pavucontrol, audacious or the friend list from pidgin (I think that's everything I have running right now). The exception being if pidgins task bar menu is open, then the cursor is the usual (small) size, no matter which window the cursor is in.
I use i3 as window manager with no desktop manager on debian Stretch (but I only upgraded a couple of days ago, and also saw the problem on Jessie).
Any explanation (and cure) or just hints to how I find out what is wrong.
Best Answer
I just discovered that the problem is actually not window-related, but widget(?)-related, the huge cursor doesn't occur when it's over pidgin chat windows (as I wrote), but only when it's over one of the text fields (which takes up most of those windows, which probably explains why I didn't realise that before), either the one I can use to type messages into or the one where messages appear.
The mouse cursor is actually also "small" (sanely sized) when over the title bar of windows. In addition I can add Chromium and Spotify (but I think I read somewhere that new versions of spotify is mostly a camouflaged chromium) is also on the list of programs that cause the huge cursor.
That all made me think that maybe this is might be due to a question of (a poor) mouse cursor theme and a fallback (that looks better) when the mouse is over some kind of window that doesn't cooperate with the parts of gnome that still infects my systems to produce the huge mouse cursor, which also explains why bvx89 reported in a comment that he saw this on a new monitor. That made me search the net for "linux mouse cursor DPI", which made me find Cursor is huge on Ubuntu due to high resolution monitor, which actually seems to be the same problem, reversed (he reports a huge cursor over "system-dependant things" and not over firefox). But his solution (i.e. selecting a cursor/icon-theme with only one size - which is non-standard but you can download https://github.com/codecat/dmzblack-96dpi that he refers to) worked for me, now my mouse cursor has the same (sane) size everywhere.