Olympus E-1 has a 5.0MP Four Thirds (17.3 x 13 mm ) sized CCD sensor . On the other hand, Olympus E-3 has a 10.0MP Four Thirds (17.3 x 13 mm ) sized CMOS sensor and features TruePic III processor.
Olympus E-3's sensor provides 5MP more than Olympus E-1's sensor, which gives a significant advantage in real life. You can print your images larger or crop more freely.
On the other hand, please keep in mind that Max sensor resolution is not the only determinant of resolving power. Factors such as the optical elements, low pass filter, pixel size and sensor technology also affects the final resolution of the captured image.
Below you can see the E-1 and E-3 sensor size comparison.
Olympus E-1 and Olympus E-3 have sensor sizes so they will provide same level of control over the depth of field when used with same focal length and aperture. On the other hand, since Olympus E-1 has 102% larger pixel area compared to Olympus E-3, it has potential to collect more light on pixel level hence have less noise in low light / High ISO images.