On San Mateo side The Counter just opened at Hillsdale Shopping Center - haven't tried that location but Palo Alto is really good.
My favorite is Godfather's on the Belmont/San Mateo border - they're awesome. Jack's Prime in San Mateo is really goooood too.
Hillsdale Shopping Center
3101 S El Camino Real, San Mateo, CA 94403
3723 S El Camino Real, San Mateo, CA 94403
On the high end, slightly exotic side, Pasta Moon in HMB has a lamb burger with harissa at lunch.
Chez Shea, also on Main in HMB has a Ranchera burger at lunch too. I have not tried it but I would consider it a good bet based on the quality of their other items.
315 Main St., Half Moon Bay, CA 94019
408 Main St, Half Moon Bay, CA 94019
The 3 Zero Cafe is a fun stop. It's at the Half Moon Bay Airport in Princeton-by-the-Sea, and has a nice aviation theme to it. This is not a Zuni level burger, but it fits the bill when I take my son horseback riding at Moss Beach Ranch.
1658 Market Street, San Francisco, CA 94102