Thought I would provide some numbers for the OP to consider. I have both of the systems (a 3,1 and a 5,1) being discussed. They're configured as follows:
2008 Mac Pro: 2 x four core, 2.8GHz processors, 6GB memory, GeForce 8800 GT, OS X 10.11.6
2010 Mac Pro: 1 x four core, 2.8GHz processor, 32GB memory, Radeon HD 5770, OS X 10.9.5
Benchmark applications: Cinebench R15, Handbrake 0.10.5 using the "iPhone & iPod touch" preset.
Transcode file: 4GB, 1080p HD video
All applications were left at their default configurations.
Here are the results:
Handbrake:
2008 Mac Pro: 50.33 average fps, 15:32 total transcode time
2010 Mac Pro: 38.25 average fps, 20:26 total transcode time
The 2008 Mac Pro is 32% faster than the 2010 Mac Pro.
Cinebench:
2008 Mac Pro: 601 cb eight threads (8 cores), 80 cb single thread
2010 Mac Pro: 462 cb eight threads (4 cores, 2 threads / core), 92 cb single thread
The 2008 Mac Pro is 30% faster than the 2010 Mac Pro.
For these benchmarks the 2008 Mac Pro outperforms the 2010 Mac Pro except in single thread performance (whereas the 2010 Mac Pro was 15% faster).