One is for enterprise specific distros (RH Enterprise, White Box, etc.), while the other is for regular distros.

Enterprise linux, as I understand it, is geared towards technical workstations/servers, built with company in mind.
Taken from
here,
QUOTE
So basically, the concept of an enterprise linux offering is that you have a fairly long time between releases (12-24 months) and a product that remains supported for an even longer period of time than the release cycle. This allows for stable server deployments with guaranteed bug fixes and security updates for an extend period of time (up to 5 years).
Don't use the enterprise kernel unless you're using enterprise linux, I suppose.

Atleast I see no reason to run the enterprise kernel over a non-enterprise kernel.