Hmm. I had a look around and it turns out I have nozzles for most of the engines under discussion in the thread laying around, as well as an F-104G kit, all in 1/72, so I did bit of comparing. No photos because I have crap lighting and I seriously need to clean my workbench, but here are some verbal findings:
General Electric J79 (Revell F-4F): Since I had the kit in the same box (60th anniversary of the Luftwaffe gift set), I figured I'd check if they were the same size. They are - though the build process is different and you can't use the Phantom nozzles in the F-104 kit without cutting off the burner can and installing it separately. It does mean that any engine you can install in the F-104, you can install in the Phantom, though.
General Electric F110 (Revell F-16C-50): Forget it, the nozzle on the F-16 is so big you could stick the J79 nozzle inside it with room to spare. While I know "physically impossible" tends to be answered with "challenge accepted", this just wouldn't work without an entirely new tail.
General Electric F404 (Academy F/A-18C): I couldn't find the actual nozzles, but it looks like they're a tiny bit smaller in diameter than the J79 nozzles. They're also longer, and in the contracted position, rather than fully open like the J79 nozzles, so they'd look very different.
General Electric F414 (Italeri JAS-39 Gripen): I actually have a Revell Super Hornet I was looking for the parts to so I could compare those, but I couldn't find it. Checking the Gripen nozzles against the tail end of the Revell kit though says they're the same size. And the Gripen nozzle is also the same diameter as the J79 nozzle. Like the F404, they're molded in the contracted position, and they're kind of long (even longer than the F404s) so they'll stick out further from the fuselage shroud thingy around the F-4's exhausts.
General Electric F101 (Revell B-1B): Tested this for a laugh, if the F-16 nozzle was large then this is ridiculous. If the B-1B nozzles were fully open, you could fit the F-16 nozzles inside them like you could the J79 into the F110... (While I was looking for nozzles I also found an F100 nozzle from Revell's F-15E in 1/48 - it's only a little too large for the B-1's engine mounts!)
Eurojet EJ200 (Revell Typhoon): The nozzles for these, while available in both open and closed in the same kit, and therefore leaving you with a spare pair of nozzles after every build, are also sadly *slightly* smaller in diameter than the J79 nozzles. You may be able to make it work however.
Turbo Union RB199 (Revell Tornado): These are around the same diameter as the EJ200 engines, but they only come in the fully dilated position, and it has those thrust reversers which won't fit inside the engine shroud on the F-104 (or the F-4). I think this would be kind of difficult to execute.
Pratt and Whitney F100 (no manufacturer): I actually don't have any of these except the F-16 version which is just as huge as the others. I have built a few F-15 kits though, and the F100 as presented on those is a little smaller in diameter. Not sufficiently to fit on the F-104 though.
Pratt and Whitney TF30 (Esci F-111A): These are, once again, a bit too large for the F-104, plus they're in the dilated position, which means they're really short and would not be visible from any aspect except the rear. TF30 engines from a Tomcat kit with converged nozzles would stick out more.. but they still wouldn't fit due to the larger diameter.
SNECMA M88 (Hobby Boss Rafale C): I didn't actually find these but I found the airframe and the part where the nozzles connect to. These are similar in diameter to the EJ200 nozzles, i.e. slightly too small for the F-104, but possibly doable.