I have flown a few jets with and without missiles and external tanks. In my personal experience there where no big changes on how the jet handled and there was no need for CG adjustmets.
I have flown the F-18F and the F-16 1/6 from Skymaster with full missiles and external tanks. In both cases besides extra drag and becoming a bit more unstable under windy conditions no trim changes where needed.
The F-18F became more sensitive with the elevator and I lowered a bit the total throws, for the F-16 no changes where made.
I also flew the Skymaster MB-339 with the underwing tanks with no changes in the flying performance, again with exception of the extra drag.
I guess it will depend on the jet model, I am sure in the Rafale for example those big tanks most probably will change the way the air moves around the wing quite a bit.

F-16: http://www.youtube.com/watch?v=-ux_tnSdMgU

F-18F: http://www.jetsrc.com/videos/F-18F_JR_2.wmv


Michel