Question: grad classes as undergrad, how to mention in grad applications?

[Troponin]

I'm in the process of getting my application to grad school completed and have a number of "5000" level classes that I'm not exactly sure how to classify on my my applications.

Is it appropriate/acceptable to list ALL of them as "graduate" classes that I've taken as an undergraduate...even though some are sort of "quasi" grad/undergrad classes?
*For more detailed reference:
5000 level classes are listed in both the graduate and undergrad catalogues, but for undergrads to register they have to get written permission beforehand.
6000 level classes are only available to graduate students, i.e., students who've been "officially" accepted into the graduate school and are currently enrolled in a MS or PhD program. A few of my 5000 level classes are "legitmate" graduate classes (i.e. 6000 level) that are listed as "Independent study: 5980" on my transcript (because of the restriction listed above).

A few other classes are also listed as "independent study," but are either one-on-one "discussion" type classes with a professor or self-study on topics needed for research I've been doing with a professor.

The rest are 5000 level math classes and an "atomic and molecular physics" next semester.

Also of note:
The math dept has a number of 5000 level classes, so it is more common to see a mix of grad/undergrad in those, but the physics dept. doesn't usually offer any 5000 level classes (the "atomic and molecular physics" class is actually the first/only one that's been offered since I've been a student here).I apologize if I'm being overly detailed, but I've really tried to take difficult classes (as opposed to more "gpa friendly" classes) and want to make sure my application emphasizes that, but I also don't want it to seem like I'm trying to inflate my stats by listing all of these as "graduate" classes when some of them might have had 30-40% undergrad students (I don't have any idea of the exact ratios, but I would guess that a class of 10 with 3 undergrads is a good representation), and others were independent study or other non-lecture style classes.I've asked a few professors and have been given varied responses.

One says that if they are listed in the graduate catalogue (even if they're also listed in the undergrad catalogue), then I should call them graduate classes.

Another says that I should just give a description of the class (since most of them are listed as independent study) and let the departments that I'm applying to decide how they want to view them.

Another says that I'm basically screwed as far as getting proper "recognition" for them because, since they're all listed as "independent study," if a department actually takes the time to review the official description of every one of the 5000 level classes...they've all but sent my acceptance letter already.

Another told me that it probably won't make much difference either way (which, if true, means I've pretty much written this novel for nothing). If it makes any difference, my gpa in these classes is good...probably 3.8 overall, with a 4.0 in the physics classes (we haven't yet received final grades for this semester though).

 

[Chaostamer]

That sounds a lot like the situation in my school. Undergrads can register for 5000-level classes but need special permission for 6000-level classes. The consensus is, since 5000-level classes are only required for grad programs, despite that they're open to undergrads, they're officially considered grad classes. I'd say that you can consider them grad classes for the sake of a grad school application.