Zener Diode for overvoltage protection
You could consider a Transient Voltage Suppressor (TVS). They are basically diode arrangements that are intended to protect circuits like yours from over/under voltages. Since they are designed to work with microcontrollers and other devices for this purpose, you can choose the voltage range you're using when you buy them (e.g. designed for 3.3V and goes into a full clamp at 3.5V).
Operational voltage ranges and tolerances for these devices are typically better than straight-up zener diodes.
Negative protection is included in the package as well. They work very well for ESD protection. There are a lot of them out there, but here is one example:
http://www.semtech.com/images/datasheet/uclamp3301d.pdf
For over-voltage protection of signal lines a zener diode is generally a poor choice. You haven't given enough details of your application for me to give many specific reasons, but you should consider the following:
A BZX84C 3.3V zener has up to 450pF capacitance. You have a 1MHz signal, which will probably be attenuated due to a RC filter effect in your circuit.
Zeners do not have a sharply defined conduction voltage. They start to conduct at a much lower voltage than the zener voltage Vz. This becomes a problem when your signal has a high source impedance, or if you have introduced some series resistance to try to limit the effects of over-voltage. To counter this you may need to use a higher voltage zener, but this then defeats purpose of including a zener.
If you are concerned about high energy over-voltage transients then a zener is of no use at all. It reacts too slowly, and cannot absorb much energy.
Generally, for signal lines, a Transient voltage suppressor is a much better part.