Will an ATMega128A work with a 12.8MHz external crystal?
You'll be fine with any crystal up to 16MHz according to that chip's spec (see page 56).  Resonators are not the same as crystals and on some chips they need to be treated differently, always check the datasheet for any differences.

Table 13-3 in the datasheet (the last row in that table) shows what settings and caps you need for the 12.8MHz xtal.

Many microcontrollers will allow you to clock them at any speed down to zero Hz and up to whatever their maximum stated frequency is.  Often a MCU will have a slow speed internal oscillator (typically 32768 Hz) for times when you want to go into a low-power mode.

One interesting example is the Parallax Propeller P8X32A chip which behaves well at any clock speed between "DC" (literally Direct Current - no oscillation = 0Hz) up to a nominal 80Mhz.  If you're careful you can even vary this clock rate on the fly and still get correct operation as long as all your edges are clean.

Many MCUs will allow you to programatically change your clock source or the "PLL taps" at runtime, sometimes for power saving, sometimes for changing other properties such as baud rate of a UART for instance.

In 99% of applications though most people will use a MHz range clock simply because they are cheap, available and provide a lot of processing power per unit time.

Further info -- related topics...


Sinusoidal clock sources
Clipped-sine crystal output (which is quite common as it approximates a square wave).
Square-wave clock sources