Breakfast in Manhattan Beach is an event amongst the locals. Everyone has their favorite place to go, and typically are regulars at that spot. And like all good places in Manhattan Beach, if it is good there will be a wait.
Uncle Bills - good food, and a great outdoor patio. There is a wait.
Hennesey's - Good breakfast and has a bar in case you want to have a Bloody Mary as well. A couple of TV's if there is a game on.
Shark's Cove - Sports bar, with a fairly good breakfast. Again the draw is it is a sports bar.
Kettle - Good food, but basic.
Good Stuff never quite caught the attention of the locals here, and went out of business. Most people would make the trip to Hermosa to eat outside with the view of the strand.
Getting away to the north end of MB, there is:
Local Yolk - great breakfast, seating outside on sidewalk, daily specials.
North End Cafe - Excellent food, but hours start at 9am. Great sandwiches too.
Pancho's - Excellent brunch in a mexican style, also serve free champagne with the entrees.
OB's - Great sports bar with a good breakfast.
Sharkeez - Great mexican food and breakfast, Bloody Mary bar, Free Champagne for 1 hour with food purchase, and TONS of TV's for sports. Gets very crowded on Saturday and Sundays during the college and NFL seasons.
Uncle Bill's is good, but nothing special. I actually prefer Good Stuff to Uncle Bill's...but I have only been to the Hermosa Beach location, don't know if the Manhattan Beach one is as good. But I'm sure either place is fine. In my opinion, Martha's down in Hermosa Beach is actually the best breakfast spot in Hermosa/Manhattan Beach. It is a 5 min drive or a nice 30 min walk along the strand (maybe 1.3 miles? I'm not sure the exact distance, but it's not long if you like to walk...I walk this route all the time).
There are other threads about this, I think, but Uncle Bill's is good, though it tends to have very long waits (there's also a counter which is quicker). I always like the Koffee Kart, too, which rarely had waits when I lived there (but could be different now). Those are the only 2 places I went to regularly. (I didn't care for the Kettle or Good Stuff)
(If you're willing to drive 5-10 minutes, Martha's in Hermosa is great, though it has waits, too.)