Click or a thunk? That's a good question.  It's a loud click and a soft
thunk.  while trying driving "smoothly" through the gears the car kinda
has this hard shift to it and jumps just a bit.  Though, the noise also
happens when I shift from neutral to a gear while just rolling and not
releasing the clutch.   So, when shifting into third, for example,
there is a click when I shift, and a click when I release the clutch.

  I too was thinking engine mounts  -today actually.  My girlfriend
drove us down to carrowinds and it was doing the same thing to her, so
it's not just me or my 'style of shifting'.   I've shifted a few cars
(any car) while the engine is off and I could hear  that mechanical
clicking of moving the parts, but this is quite more audible and while
the engine is accelerating.

 When the clutch pedal comes down and there is, for lack of a better
descriptiion, positive torque coming out of the transmission (making
the car go forward instead of a down shift) the thunk is heard.
However, I can shift into a 'new' gear and it will make the same thunk.
 not a loud thunk, more of a clunk (click-thunk).  By 'new' gear I
mean, if I'm in second and goto neutral then go into third it will
thunk, but if I go back to neutral and into third again it won't.
Everytime I release  the clutch pedal when accelerating ("positive
torque")  and the pressure plate (flywheel?, clutch plate?, pressure
plate?  ....I need to look this stuff up!!)   grabs the transmission
there is that thunk.

  This leads me to think transmission, because it does it when I shift
to a new gearl.  I've changed the tranny oil even though the old stuff
looked fine.   Is there anything that can go bad in there or get worn
too much that could acount for what I hear?    The master and slave
cylinders were changed out two years ago, so I don't think they would
go bad, or be a culprit of what I hear.   There is no slipping or
anything similar.

  I've helped change CV axles on my car before, so I kinda know what
it feels like to get that pop when the axle end seats into the
transmission.  I never had any probs from those old ones until I needed
to replace them many miles later.   I put these new ones in back in
March and with over 1500 miles since then I have only recently heard
these noises.  I don't think it's the CV axles

there maybe a coincidence thing going with the engine mounts.  They
may be failing, but if so I believe it is slight.  I'll check them by
observing the engine while someone starts to drive the the car, but I
doubt it is the problem.

   Thank you ALL for the responses and questions.   Your help and
suggestions benefit me tremendously (as well as the cautions).