First of all, don't forget to take advantage of Fast Pass. Even if you get the Passes earlier on in the day, keep them until you want to use them (in the same day). The rule is, as long as you don't come before your comeback time, they really don't expire. We used ours as late as 3 hours after our expiration time.
Next, there are a couple of lines that might seem long, but they go pretty fast. At
Disneyland, check out the Jungle cruise, Pirates, Haunted Mansion and Buzz lightyear astro blasters. I think Haunted mansion will be closed for refurb.
Also, I agree with some of the posters- Big Thunder Mt. RR. is great at night! My boyfriend is a definate fan of it!
You can get a good seat for the Pixar Play Parade pretty easily. So, maybe 20 min ahead of time, or even 15 would work. It's a water parade and the water shoots pretty far. For the disneyland parade, maybe 30 min, if you're waiting until the last minute. 45 would be better. I'm not sure how long each are. Hmm.. although, I think weekdays in Sept would make those wait times less. They probably last about 20 min. I'm not too sure.
Check the map and schedules for that day to determine which way the parade route will be or ask a cast member. Knowing the routes will help you get a good seat too because people tend to sit where there are people sitting already so there are generally gaps that people don't sit (mabe they don't know it's part of the route).
Good Luck