I pulled apart a FUJI temperature controller many years ago and found they used a LM324 as a integrating a/d along with a micro. Most people I knew doing this sort of thing used a AD595 as Steve suggested and fed that into an a/d. I've recently used a ADuC834 which is a 8051 core,62k flash,4k eeprom and a 24 & 16 bit a/d converter. This will convert the microvolt signal directly from the thermocouple (you'd want some input protection though!). They have some newer parts with a faster cpu and analog mux etc. This would probably turn out cheaper than the AD595 & cpu (AD595's aren't known to be cheap!). Analog Devices are good for the samples although it is a small surface mount part I would suggest the eval board to make things easier.

Or there's Kai's suggestion of an op-amp and do it all analog.