Connectivity
Both models have Wi-Fi connectivity, but the 1000 also has an infrared port. They each have USB compatibility, but only the PSP 3000 can take advantage of the higher speeds that USB 2.0 offers. There is also TV output on the 3000, allowing you to play PSP games on your television.
Dimensions
The PSP 3000 is much slimmer than the 1000, with a depth of 18.6 mm. It weighs less at 189 g compared to the 1000's 280 g.
Specifications
The PSP 3000 has an improved screen with a greater contrast ratio and better response time than previous models. The 3000 has 64 megabytes of internal RAM as opposed to the 1000's 32 MB.