Toyota is the undisputed world leader in hybrid vehicle sales, so it's no surprise the company dominates the charts when it comes to patents for "electric propulsion vehicles." A recent study conducted by the Japan Patent Office on global trends in the EV industry found that 76 percent of the 16,670 patents filed for electric propulsion vehicles (here defined as pure electric vehicles, hybrids and fuel cell vehicles, yet excluding railroad vehicles) came from Japanese companies.
As you can see in the tables above (unedited version here), Toyota has filed dramatically more patent applications than anyone else. What's surprising is this this list only takes into account patent applications filed from 2001 to 2006, which is after the Prius debuted. Many more applications were filed in this time frame than in 1995-2000, and the numbers are still climbing.