Depends on what chassis it is going into.
Exactly... This is most important...
First, this is a dumb question, cause a decision cannot be made on the engine alone... Most will simply side with what they have owned/currently own.
IMO:
B-series in Civics and Integras
H-series in anything but civics and integras
Why? Cause of weight bias and torque... U don't need gobs of torque in a lightweight civic... Unless you like replacing axles and tires on a regular basis...
And the answer is not always bigger is better, (as some of you have said) but what will work best for the application... Just look at American car manufacturers, enough said.