cantrips:
Arcane Mark should be standard use.
Mending can be used to authenticate identity. Take a small object. Break it in half. Give one half to one person and the other to another person. When they meet, have one of them cast Mending. If one of the halves is counterfeit, it won't work.
Message is an effective communication spell, good for coordinating groups of guards or individual agents.
first level spells:
Alarm (the silent kind) is great... with many, many uses for keeping track of people and places secretly.
Charm Person - obvious. Does the Watch need to be intimidating? Not if you think they're your friends...
Disguise Self - do you really need Dopplegangers if you have this and Charm Person?
Erase - good for getting rid of inconvenient evidence.
Silent Image - too many uses to list.
second level spells:
Alter Self - when a disguise isn't good enough.
Detect Thoughts - duh.
Locate Object - coupled with tokens that can be slipped onto people surreptitiously.
Invisibility - no comment
Rope Trick - an amazingly good place to stake out an area from.
Also note that Bards make good agents in a situation like this... with spells like Alter Self, Calm Emotions, Detect Thoughts, Hold Person, Invisibility, Suggestion, and Tongues as second level spells it is hard to go wrong. Beguilers are even better.
-Stuart