Well,  I'm particularly fond of the MegaDonkey from mega-donkey.com  It does 
everything I want a microcontroller to do (it should,  I designed it).  Atmel 
ATMEGA2561,  256K flash,  8K RAM,  LCD 160x80 graphics touchscreen display,  
two serial ports,  IIC ports,  A/D ports,  lots of I/O pins,  beeper,  
prototyping area,  wonderful open-source software,  makes Julianne fries,  
gives a fair backrub.  The softwware is in avr-gcc so you have a full blown C 
compiler.  There is also a version with a Mega128 chip (128K flash,4K RAM,  
128x64 LCD,  mediocre backrubs) and one without the LCD.

The software has a software time-of-day clock with crystal freq calibration 
capability.  Has demo routines for digital and analog clock displays.  
Internally it runs off a 10 KHz interrupt so you can get that level of 
resolution.  You could add a battery backed IIC clock chip (we have a couple of 
circuit boards floating around,  haven't written the software yet).  Also there 
is a 8 pin SOIC chip pad area in the prototyping area where a clock chip could 
be added).
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