Well if you want to ride Finding Nemo Submarine Voyage go there first. If not I'd say first go to Tomorrowland. If the line for Space Mountain is more than 30 minutes, get a fastpass. Another thing I've noticed about Disneyland is that the lines are usually 5-10 minutes shorter than advertised. Anyway, after Space Mountain (or after getting your fastpass) go to Star Tours and Buzz Lightyear, since you're in the area. That's also the time to go to Autopia and Honey, I Shrunk the Audience if you want to. After that head to Adventureland. Hopefully Indiana Jones won't be too crowded, so ride that. If it is either get a fastpass, and if you already have one for Space Mountain just wait until later. Then go on Jungle Cruise, Enchanted Tiki Room (if you want), Pirates of the Caribbean, and Haunted Mansion. After Haunted Mansion go to Splash Mountain, Winnie the Pooh (if you want), and Big Thunder Mountain Railroad. Then go to Fantasyland and ride the Matterhorn Bobsleds. If you got a fastpass for Space Mountain or Indiana Jones, you should be to use it now. After riding one of those go back to Fantasyland and go on all the dark rides. Oh, and another note about the Matterhorn- don't be afraid if the line is halfway around the mountain. The load speed is fast and I've never had to wait more than 25 minutes.
Have a great time!
-Evan