12 bit vs 14/16bit ADC for ph sensor interface
Like JustJeff says, if you design your circuit for a pH range of 6 to 9 you have a resolution of better than 0.001 in 12 bits. If you want the full pH 0 to pH 14 range your resolution will be  


  \$ \dfrac{14 pH - 0 pH}{2^{12}} = 0.003pH/LSB \$


You can achieve 0.001pH by using a 14-bit ADC.  

But it's important to draw a distinction between resolution and precision. Example: a digital fever thermometer which you can buy for less than 10 euro. This gives a reading with 2 decimals, like 36.87°C. But is that also the precision? In other words, is the "7" correct? No it isn't. It's even possible that the accuracy is worse than 0.1°C.
The same goes for a pH meter. You can have a reading with 3 decimal digits, but don't expect this to be the precision, think about the quality of other electronic parts.  

edit
Also keep temperature compensation in mind. Temperature variations will cause the pH to change, and also change your probe's reading. Unless you have a highly accurate temperature reading it's no use going for better than 0.01pH precision IMO. Good temperature measurement isn't a sinecure in itself. This site says  


  "[The] temperature error is very close to 0.003 pH/°C/pH unit away from pH7."  


So at pH 10 a temperature variation of 1°C will result in a reading change of 0.01pH.