My experience lately is that the line for Nemo is getting pretty short i.e. 30-45 minutes the closer you are to park closing. I think Nemo is still a ride people are waiting to rush to right at rope drop.
Especially when you factor in the long vacations that will be hitting from this weekend on... That means a lot of first timers who haven't yet experienced the wonder that is Nemo.
Free advice... You get what you pay for.
Check out My Roller Coaster Tycoon 3 rides... I'm always working on another one... I hope they make you want to go to Disneyland.
FWIW, we got in the sub line at 11:38 PM Sunday 11-11-07 and were loading in 30 minutes. When we got off, the line was clear. For a 9AM opening, there will likely be a rope drop after opening Main St. at 8:30. Because of this, instead of a stream of people entering the gates at opening, a MOB of people will flood the park instantly, so lines will build up much, much, much faster; especially those 2.
We only went for 1 day, and skipped PP to ride the subs at opening and close. If you must do both, I'd do 1 in the morning, and one in the evening. I also liked the subs better at night.
EVERYBODY will make a beeline straight towards Nemo. Go to Peter Pan first (don't even bother passing by Nemo) and the Peter Pan line will be about 20 minutes long. Any other time in the day it'll be about 45 minutes long.
I got to DL at rope drop about a month or so ago. Goofygoof and I went straight to Nemo and it was already over an hour long. We decided to skip it and power walked to Peter Pan. The wait was 20 min. (the shortest I've ever seen it).
If you're going to be there all day, I'd hit Pan first and hit Nemo around closing. It seems the line is pretty steady for Nemo even at opening, and you can hit Peter Pan, Dumbo and quite a few other Fantasyland rides in the same amount of time you're waiting and riding Nemo.
I agree with all those who say to go to pan first. Peter Pan has a freak mutant line which is only short at opening. The only other time I've had any luck with is right after fireworks, when they're reopening Fantasyland, but most people use that time to head to Fantasmic.
And, as others said, subs appears worst in the morning, and at least gets a little better in the afternoon. And, I think, it's easier to wait for, probably because of the longer ride time.