Use AVR Atmega like a 555 for timer
No, without any (meaningful) program the MCUs don't do anything useful. 

As Brian pointed out, you can definitely write a program that samples analog quantities (voltage on certain pins) and perform some tasks or generate digital outputs according to the read values. It might mimic 555 or do anything even more complex.

However, I'd say that mega128 are pretty much overkill for such task.