Should I use 2 GB of DDR2 1066 RAM instead of 3 GB of DDR2 800 RAM on Windows 7 64bit?

Does your motherboard support 1066MHz memory? If it doesn't the 1066 will default to 800MHz. Use this to find out. http://www.crucial.com/
It'll also tell you if your system supports dual channel memory. If it does and you're using 2 memory modules of 1@1GB and 1@2GB it's not operating in dual channel mode, but rather the slower single channel mode. In order to operate in dual channel mode you would need to use a matched set of memory, such as 2x1GB of DDR2 800MHz or 2x2GB of DDR2 800MHz, etc. If your motherboard supports the 1066MHz memory and you have only 2 memory slots, get 2x2GB not 2x1GB. 64 bit operating systems are able to address larger amounts of memory than a 32 bit os, so install more memory than you have now, not less.

2Gb (1066) is better.

Actually when you put two rams with different specifications ,system will take the lower as default !

it will be a little bit faster, not worth 1 less gb. you could always put the 2gb and 3gb ram in, the speeds will default to 800mhz.