Formal:
* Assistant
* Clerk
* Administrative Assistant
* Executive Assistant
* Personal Assistant
* Aide
* Office Manager
* Administrator
* Officer (in some organizations)
* Minister (in a government context)
Informal:
* Helper
* Right-hand person
* Go-between
Other:
* Scribe (historical)
* Amanuensis (historical)
* Note-taker
The best synonym to use will depend on the specific situation and the type of secretary you are referring to.