Here are my initial thoughts; I can spend some more time this weekend.
I've got them both hooked up to a TivoHD at the moment; this is my only HD source since I don't have a Blu-Ray player. I've got the Samsung connected via HDMI and the Panasonic via component. I'd rather have had them both use the same connection type, but it's not an option given what I've got to work with. FWIW, I tried the panasonic using both HDMI and component and couldn't tell a difference. I sit about 9 feet away from the 2 sets. For anyone who doesn't know the specs, the Panasonic is a 720p (1024x768) 42" set; the Samsung is a 1080p 46" set.
After some tweaking, you can get the two sets to look pretty similar in terms of overall brightness and color, though there are some caveats about brightness below. I'm sure a proper calibration could help more. Compared to the LCD, the plasma seems to have a slight greenish cast to it when there's any ambient light. You don't tend to notice this if you're just viewing the plasma by itself, but compared to the LCD you do see it. It seems that you ought to be able to get more accurate color on the Samsung; it doesn't seem to have too many weaknesses here and it's got more flexibility in the setup menus. In any case, while there are differences, I personally didn't think that color was a big reason to prefer one over the other; after tweaking they are more similar than not.
Here's an oddity regarding brightness. It's actually difficult to get the two sets to look equally bright on all scenes. Let's say I tweak backlight, brightness, etc. so the two sets look equally bright on outdoor scenes. The LCD will still look brighter if a very very bright scene appears, and oddly the plasma looks brighter if there is a mostly dark scene with a bright area. I suspect this is due to the way plasmas' maximum brightness varies with the scene, since it doesn't seem to be my eye playing tricks. But it makes it a bit difficult to compare the two.
While the plasma is capable of producing a deeper black, the settings I've got now seem to be crushing blacks a bit on the LCD. I haven't been able to tweak this out yet. This actually results in a deeper looking image on first glance. After a little while you realize that the loss of details makes the LCD image harder on the eye; I find myself straining to look at the image sometimes. What ends up happening is that scenes without true blacks look deeper and have more pop on the LCD, but this seems really bogus to me and I find it difficult after a while.
If you're sitting very, very close, the LCD looks smoother due to the difference in pixel structure and the lack of temporal dithering. In stores I noticed this and actually thought I had a strong preference for the "look" of LCD. At my normal seating distance, this isn't an issue anymore.
I think folks who say "you can't see the difference between 1080 and 720 at 8-9 feet" are overstating the case. In practice, you can tell, it's just not a big difference. The only time it's really noticeable to me is on computer-generated graphics like station logos, sports score boxes, etc. On program material, I don't find it to be much of a factor and certainly wouldn't consider it to be an advantage for either set. YMMV.
The mpeg compression artifacts are more visible on the Samsung. I need to look more closely at some video to see why. This could easily be explained just by the lower resolution and smaller size of the Panasonic.
The Samsung has a semi-matte screen, the Panasonic has whatever they call their latest anti-reflective screen. In my room, they both reflect about the same amount, but the Samsung's reflections are more diffuse and blurry while the Panasonic's are sharper and have that funny double-reflection thing going on. I don't prefer one over the other very much, but I don't have much lighting or direct sunlight where it would be a problem. In another setting, this could be a huge issue for someone. I probably should have tried an LCD with a glossy screen, given my setup.
The gloss black finish on most HDTVs these days really bugs me. I'd rather have my TV look good turned on than turned off, but whatever. I really like the cheapo matte-black finish on the Costco plasmas.
Viewing angles are a real issue for our room. We have a sofa running along the side wall, and there's just nothing the Samsung can do about that. All my comments above about the two sets looking similar go out the window. In fact, the more you tweak the Samsung to look good on-axis, the worse it looks off-axis. I think the off-axis performance is not so bad when you've got the LCD tweaked for a very bright situation, but if you've got it set up for moderate light, it really washes out. You don't have to move far to see it, either. If I move around so my head is even with the left edge of the screen, the black level on the right edge actually increases slightly.
The odd thing is that in side-by-side viewing, I often find myself more impressed with the LCD. I can definitely see why people come away with the impression that LCD produces a better image; it's much easier to make it look impressive. However, what seems more impressive about it also makes the image a bit harsher. The brightness isn't much of an advantage in my room, since I've only got two windows on the side of the room which don't get direct sunlight shining through.
In a dark room, the plasma really just looks a bit better in every way. The difference in black is pretty significant, although the Samsung isn't bad at all. In even moderate lighting though, the difference in black, while noticeable, isn't a big deal.
Overall, the plasma seems softer and more natural; the LCD sharper/harder, capable of being much brighter, and harsher. It seems like you have to do a lot of work to get the LCD to try to do what the plasma does more naturally. This has been pretty consistent no matter how I've tweaked the settings. In bright light, the differences between the sets could definitely work to the Samsung's advantage; it is certainly capable of being much brighter. All in all, the differences in moderate light aren't huge if you're sitting on-axis. I know I listed a bunch of differences in my notes above, but in real life these are not huge differences. Overall I think the plasma makes a better image in my room, but it's actually much more difficult to choose between them than you might think. I do most of my watching these days with some ambient light. If I watched mostly movies in a dark room, I think it would be more clear.