Breakfast in San Jose???
I second Southern Kitchen, the one on Monterrey Rd. The one in Los Gatos is great, but you've got to stand on line on the weekends. I like Bill of Fare because they have raisin toast. I think it's worth noting that they don't take credit cards. If you can handle Bill of Fare, you might consider the Fourth St. Bowl, on 4th St just north of 880. It's a serious greasy spoon, but every now and then I feel the need to have their linguica and eggs.
If baked goods are enough breakfast for you, try Fleur de Cocoa in Los Gatos. IMO, this place has hands down the best croissants in the bay area. His almond croissants are masterpieces, especially if they're still slightly lukewarm. They also serve coffee, espresso, and rich French hot chocolate.
My husband and I love Bill of Fare off of Saratoga and Williams right behind a Rotten Robbies. It's on the dive-y side and really charming. The decor is a combination of car posters and family knick knacks. Love it!
As for the food, the oatmeal pancakes are fantastic. They also have some pretty ono Portuguese sausage and if you want to go all the way on the Hawaiian style, you can even get some good sticky rice instead of hash browns.
Pam's Eastside Cafe on McKee near Jackson is worth checking out, especially if you are diabetic. They have special sections in both breakfast and lunch/dinner menus for low-carb, no-sugar options, and offer many no-sugar drinks not found elsewhere. Their coffee is rather weak, although homefries and omelets are pretty good, if not in the same realm as Berkeley's Homemade Cafe. We are still looking for a South Bay equivalent to that.
Lately we have been devotees of the Pomegranate Cafe on San Fernando between 4th and 5th, across from SJSU. For $3.50, you get a good mushroom omelet, some homefries and a slice of toast. The portions are just right, not the mega-size usually wasted. Plus all coffee is Vigal machine espresso, and the lovely owner always has a wise and kind word.
There really aren't any breakfast places I would call gems in San Jose; I think it actually is one of the worst breakfast towns on the planet!
That being said, here is the list of places I tend to end up at...
Southern Kitchen – Very, very busy. I like their French toast and pancakes. Expect a long wait on the weekends, but probably worth it as this is one of the better breakfast places in the area. 27 Main Street, Los Gatos.
Los Gatos Café – Go here for the gigantic and really good omelets. Also very popular with long waits, but worth it compared to the long waits/bad food at a lot of other breakfast places. 340 N. Santa Cruz Ave.
Original Pancake House – even though it is a chain, I love the potato pancakes, Swedish, and Dutch Baby. There is one near Curtner/87 and one in Cupertino.
Southern Kitchen – Not even remotely related to the one in Los Gatos. Huge portions at really reasonable prices. Sounds crazy, but I LOVE their fried chicken breakfast, served with awesome grits and weird orange from-a-box-mix Swedish pancakes. Southside, 3378 Monterey Road.
Lowry's Irish Coffee House. I like this place even though the menu is pretty limited and the service and food can both be hit or miss. Good coffee, oatmeal on the weekends, Irish breakfast sandwich. 350 West Julian St, San Jose
Country Gourmet. Decent California style breakfasts; I like the English banger sausages and oddly crispy biscuits. 1314 South Mary Avenue in Sunnyvale.
Mini Gourmet. Open 24 hours and a San Jose institution. Not much else to say about it. 599 S Bascom Ave.
Cardinal Lounge – Reno décor in suburban San Jose, and I think one of the only other 24 hour breakfast places in town. Huge menu, huge portions of average diner food. Weekdays they have a decent $4.25 menu. 3197 Meridian Ave.
A Bite of Wyoming: Atmosphere, buffalo steaks and eggs. 2227 Alum Rock, San Jose
Stacks: mini-chain in the Peninsula. The Campbell location always has huge lines of people on the weekends. I’ve never really figured out the attraction, but obviously people like it. I think there are others in Menlo Park and Redwood City.