Hmm... glad this is all opinionated...
COUPES:
Bone stock Vs. Bone stock: I'd pick the 6th gen. The 7th sometimes looks too high. 6th Gen > 7th Gen
Vs. 6th gens at a glance: I love the body lines on the 7th better. I don't like door moldings. I just love how the shape from the side is a lot more sleeker. (For instance the trunk, to the windows to the front fenders line up nicely and the lines of the cage is sleek.) The body of the 7th gen looks to be a bit larger but I wonder why with some models it's a few 100 lbs lighter? 6th Gen < 7th Gen
Front and rear: Perhaps where the 7th gen loses as this also seems to be where the cars will stand out the most or look like everything else. The front design of the 01-03 Civics is ok, but entirely the design of the 99-00 is better. I actually like the 01-03 headlights. The front bumper is plain but I can't say it's ugly or really special. The grille again is okay but there are better. As far as the 04 goes, the headlights are Toyotas, the front bumper is a smaller, more defined version of the Civic Hybrid sedan (I don't like bumpers that smile), but the grille looks fine. The lines on the hood are now a bit deeper which is nice. The 04 shows that the new Civic further loses more of it's uniqueness.
The rear... hands down, 6th gen. Don't think anyone would really disagree that the 99-00 red/white tails were simple and clean. I also like the OEM rear lip. The 7th gen gets a totally different approach. It's brake lights appear to be the shape of the "C" from the new "CIVIC" emblem, and at first I thought that was sort of cool. Although the trunk lid shape is still similiar to that of the 6th gens, the tailight shape... and among other things up front convinced a lot of people that the new Civic looked like a "Baby Accord" (6th gen). lol The 04 gets new tails that're now 3-D-ish (think Altezzas), and are bright red, replacing the C with a brake light that appears to be like a larger turn signal. I don't like that they're transparent... in fact, I'll keep my stock 02s. The rear bumper however is what I like. It's design however is nothing new from Honda, but it's lower thus is lines up with the body better. 6th gen > 7th Gen
OEM lips/body kits: Tough call... but I think the 6th gen edges out. The new 04 kit looks a lot better than the 01-03, but I did like the 01-03 rear lip. The front looked a lil' too bulky. 6th gen > 7th Gen
Interior: 7th gen wins. There's not much difference to it except the 7th gen... especially the 03+ have better gauges. The layout is almost the same between 6th and 7th gens but I'll have to say 7th Gens. I don't really have a good reason for it. Oh yeah, I forgot to add, the 7th gen has more leg-room front and back. 6th gen < 7th Gen
OEM spoiler: Although the 6th gen can pull it off a bit better, WINGLESS CIVICS OWN. 6th gen > 7th Gen
Lowering: The body of the 6th gens look like they can go lower over the wheels, but regardless you'll know how good the shape of your car is once it's closer to the wheels. Both cars look exclusively better but 7th gens win here. Only because from stock to say "slammed" they look a LOT different and a lot better. IMO, it looks a bit sportier. 6th Gen < 7th Gen
The suspension thing: I've never owned a Honda that was double-wishbone or to say the least, MacPherson-less up front. What I understand is that the MacPherson design up front is not as desirable to tune as well as the fact that it's an older and cheaper design. In the end, I don't think this means the 7th gens are bad handling cars when in fact they do handle quite good. I don't know what the weight distribution for the 6th gens were front and rear, but the 7th gens are 59/41 I believe... almost perfect for a front-engine, front-wheel drive car. I can't really give an opinion. 6th Gen ? 7th Gen
In the end: The 6th gen is now an 8 year old design, although the coupe will always be a favorable car to look at (99-00s especially), like it's direct cousin the 3rd gen Integra it is beginning to show it's age starting from the inside going out. I remember reading somewhere that the person (or people) who designed the 7th gen is different than the person who did the 6th gens.
BTW, you guys can copy and paste and/or add your own kind of categories from mine.
Sedans? Hatchbacks? Without going into detail I favor the look of both as 6th gens, however in my eyes, the sedan's look ages the fastest while the hatchback can somewhat hang with the coupe.