Only the cache.
The T4200 has 1MB and the T6400 has 2MB (both per core).
They both share the 2GHz Clock Speed, 800Mhz FSB, 45nm lithography, no Hyper Threading (which is good in this ones) and everything else.
From the links below you will find the required information. You can even compare the different processors that you want.
The only difference I can find here is that the T6400 has 2MB cache and it is a Core 2 Duo Processor.
Also with the new Intel processor ratings, the T4200 has only a 2 stars ratings whereas the T6400 has a 3 stars ratings, making it better. But this depends on the usage.Link: http://www.intel.com/consumer/rating.htm
On the overall, personally I would recommend the T6400 as it is a Core 2 duo, it will definitely perform better than the T4200 which is only a Pentium processor.
Hope this will be helpful.
Just for the note.
There is no difference in the architecure of a Core 2 Duo or a new Pentium dual core like the T4200 which is built in 45nm.