The thing to remember is that hybrids and electrics tend to moderately trade off emissions for an increase in toxic waste from production. Neodymium for motors, tantalum for capacitors, lithium for batteries - all of those are bad news bears for the environment. Even stuff like copper isn't particularly awesome to produce. All other things being equal (mileage, emissions, etc), you should prefer the vehicle with a simple aluminum frame and engine over the high-tech wundercar because the impact of producing and disposing of it is lower.

To the actual question - yeah, diesels running on biodiesel actually produce less GHG emissions than even hybrids. Ultra Low Sulfur Diesel is pretty close but just a bit above hybrids. The National Academy of Sciences published a study back in 2010 on the topic. The report itself is paywalled but there's a copy on the Arkansas state website. I snapped an image of the chart for ease of viewing.

Note that ULSD was only introduced in the US in 2010 (2006 for Cali). The Euros have had it for quite a bit longer. So when you're reading studies, if it predates 2010 and it doesn't specifically say ULSD or Biodiesel then you should disregard it, because the new fuels are vastly cleaner and the playing field has shifted dramatically as a result. Biodiesel is often notated as something like B100, B85, or BD20 denoting the percentage of biodiesel in a mixture with fossil diesel. Pure B100 has a fairly high gel point and can cause problems starting in cold areas, so these mixtures include a fraction of ULSD to lower the gel point.

http://imgur.com/FEOo1zB

http://1.usa.gov/1gO9jPL