Good question, i wouldn't know for sure but saeems like the NES needs some cleaning.

If it is a new TV it will probably get better with time as well.  It takes about about 30-40 hours of viewing time to break in a new LCD TV so that  should account for part of it as well.

I used to have my NES connected to my LCD widescreen TV.  Here were my observations

1)  You cant play any Zapper games.   This pretty well known but it bears mentioning again anyways.  I'd like to know if the same issue happens with Plasma (I assume yes).

2) You will usually see regions of the screen that the developers didnt think you would see around the outside edges.  These often appear as glitches, junk data, or empty data. For example, usually the 8 or so pixls all around the screen arent visible (I forget the actual amount)  so sometimes at the top of the screen you see junk sprites, or along the left and right of the screen a sprite will just disappear.

3) Newer model TVs like LCDs are more sensitive to the "bad palette" bug.  There is a color in the NES palette that developrs could use but apparently should not have used in their games.  It was used in the Game Genie, Sudoku and a couple of other games that slip my mind and can cause the TV to jitter around in an almost unplayable fashion.

Edit - Last comment.  I never really noticed anything else too weird.  Keep in mind however that the 2 different output types for the NES can have different looking outputs.  I never played any games where I noticed it though.    I also used to find that my reactions are slower on a LCD.  Maybe its the bigger screen that I'm not used to, maybe its because I'm further from the TV, maybe I'm getting old and slow, but I still prefer to blame the hardware.

Al