Cafe where Beverly meets with Trevor Grant to talk about her secret plan in episode 4x08 "The Ex-Files".
Vala is working at a diner when the place is robbed by thugs and she beats them up in episode 10x08 "Memento Mori".
Diego visits a cafe and asks if Kit Nelson has been in to order cherry pie in episode 1x03 "Kit Nelson".
Source: IMDb