While I was in Palo Alto, a friend recommended meeting at Philz Coffee right off of University Avenue—it's one of the most atypical coffee shops I have visited. They have large list of coffees from around the world and once you select your coffee they make it right there—drip by drip—so you have a fresh cup of coffee made just for you. They will also add milk and sugar for you, and if you are feeling like you want an extra kick with your coffee they will add fresh mint.
If you don’t like coffee they have a great tea selection. I ordered a Chai that was a perfect blend of spice and sweetness.