Sigma SD1 has a
15.0MP APS-C (24 x 16 mm ) sized CMOS (Foveon X3) sensor and features Dual True II processor. On the other hand, Nikon D5000 has a
12.0MP APS-C (23.6 x 15.8 mm ) sized CMOS sensor and features Expeed processor.
Another difference between these two cameras is that Sigma SD1's sensor lacks anti-alias (Low-Pass) filter. Removing anti-alias filter increases the sharpness and level of detail but at the same time, it increases the chance of moiré occurring in certain scenes.
Below you can see the SD1 and D5000 sensor size comparison.
Sensor Size and Resolution Comparison image of Sigma SD1 and Nikon D5000 Cameras
Sigma SD1 and Nikon D5000 have almost the same sensor size, so neither of them has any significant advantage over the other in terms of providing control over depth of field when used with the same focal length and aperture.
Sensor size sets the circle of confusion, so it drives how much depth of field each
of these bodies gives you at a given aperture. You can calculate it exactly for the
Sigma SD1
or the
Nikon D5000 ,
including hyperfocal distance.