I like Submarine Voyage at night not just because the line is so short, but because the exterior lagoon portion of the ride looks much cooler when it's all lit up at night.
Do the stuff that doesn't exist at WDW, or is a Disneyland exclusive and doesn't exist anywhere else in the world. For instance:
Ride the Sailing Ship Columbia around the Rivers of America instead of the Mark Twain Riverboat. Go down below decks to see the crews quarters and the maritime museum, but only after you've passed Fort Wilderness and Hawkeye (the Captains lookout) has fired off the "two cannonball salute" from the forward cannon. Plug your ears!
If you are feeling athletic, paddle a canoe around the Rivers of America on the Davy Crockett Explorer Canoes. The perspective of the scenery is quite different from that low level, and the college guys in buckskin who work the ride are jokesters for the men and eye candy for the ladies.
Don't miss all of the dark rides or smaller attractions that are exclusive to Disneyland;
Alice In Wonderland from 1958
Mr Toad's Wild Ride from 1955
Pinochio's Daring Journey from 1983
Roger Rabbit's Car Toon Spin from 1994
Monsters Inc. Mike & Sulley To The Rescue! from 2005 and in DCA
StorybookLand Canal Boats from 1955
Casey Jr. Circus Train from 1955 (and a faster way to see StorybookLand)
Tarzan's Treehouse (the Robinson's were evicted back in '99)
Main Street Cinema and Penny Arcade (not everything has to be a shop)
Check out Pirate's Lair on Tom Sawyer Island and see what all the fuss is about. Don't miss the spooky Deadman's Grotto caverns with the special effects and animatronics.
Ride the Disneyland Railroad, but make sure you travel between Tomorrowland and Main Street USA to see the Grand Canyon Diorama and Primeval World. Try and catch Walt's personal VIP car, the Lilly Belle, being pulled by one of the three or four different trains they run each day.
Don't miss the E Ticket headliner attractions that have been designed and built to be very different from their WDW cousins. In no particular order:
Pirates of the Caribbean (see where the missing 7 minutes went)
Haunted Mansion (the floor actually drops instead of the ceiling going up)
It's A Small World (a longer ride with an outdoor garden section)
Disneyland Monorail (a 1959 attraction first, and 1961 hotel transportaion second, but still fun in 2009!)
Space Mountain (the sleek 21st century version!)
Enchanted Tiki Room (the original 1963 show)
And finally, there's the big E Tickets that only exist at Disneyland;
Indiana Jones Adventure
Matterhorn Bobsleds
Finding Nemo Submarine Voyage
Over at DCA, you won't want to miss the Blue Sky Cellar Preview Center. Also check out Flik's Fun Fair, California Screamin', Paradise Pier, Disney Animation Pavilion, Grizzly River Run and Tower of Terror for attractions that don't exist in WDW or are very different in their California form.
The Aladdin musical in DCA's Hyperion Theater is not to be missed.
And don't forget to stop one night on your way out of Disneyland and look for the lamp in the window above the Fire Station. That was Walt's private apartment, and the light is kept on in memorial to him.
