One man's obscure app is another's famous bigtime one, so apologies if some here aren't 'little-known'. Most of the stuff on this thread is unfamiliar to me, but there's more than one that I thought was huge and didn't know anyone was living without.
So I'm actually including a couple of things that I don't usually think of as obscure.
A variety of things which slap friendly frontends on scripts:
Xdialog
gtkdialog
gxmessage
yad
All have a variety of strengths and, unfortunately, weaknesses. (Xdialog is supposed to be a graphical 'dialog' but you have to be ultra-careful and limited to be compatible; gxmessage is a much closer dropin for xmessage; yad is an enhanced DE-independent fork of zenity; gtkdialog is kind of in its own weird universe.)
Lightweight partial replacements for heavier famous things:
dtach - allows detaching a process from a controlling terminal without the interference of 'screen' (dtach irssi!).
mtpaint - nifty app that lets you do a tiny subset of gimpy things without the behemoth that is the 'gimp'.
Familiar things with extra features (still light!):
dwdiff - awesome app until 'diff' incorporates its features - generate (optionally colorized) word diffs rather than line diffs (like git diff --color-words).
htop - scrollable virtuoso of process monitoring - I don't use 'top' interactively anymore.
par - I still don't know how to really use this properly but it's an ultra-'fmt'.
Misc stuff:
gcolor2 - DE-independent color picker; style html pages or gtk widgets or whatever.
id3lib - this is a library, but it also comes with a handful of very basic CLI tools that are useful for any of your music that's id3-tagged: id3info, id3tag, id3convert, id3cp.
openrdate - if you want to sync your clock without a daemon (probably other ways to do this one).
rlwrap - ed with command line editing and history! Any app can be automatically made a readline app with this wrapper which, unlike most wrappers, works really well.
root-tail - display logs, etc. to your root-window.
shntool and
shorten - listen to shorten files (that you might get from etree and so on) and/or losslessly convert them to wav and then flac and otherwise manipulate them and other file formats.
xclip - read and write data from clipboards and files; as one example, some x-terminals can activate links but I actually find this annoying as it makes what should be plaintext a mousey hotspot instead (I use mrxvt which doesn't/can't do this) - with '$BROWSER "`xclip -o`"' bound to key and mouse in fvwm, it can turn any text into a link without messing with the text.
All of these are available from SBo - I'll have to think and look to see what obscure in-system stuff I use (it's hard for me to think of most in-system stuff as obscure because it's
right there.
)