Actually in the new series is appears all sides take advantage of Rail Guns and missiles rather then energy weapons as the old series did, probably to fit more in with the retro-tech aspect of the show. It seems that most if not all the offensive weapons on capital ships in the new series either have missiles, flak cannons, or rail guns/mass drivers as main offensive weapons (With Battlestars prefering railguns and Basestars prefering missiles). And while the Galactica cannot take down a basestar on it's own as seen in many episodes, the Pegasus is a different story.
as seen in the recent episode in which Apollo is promoted, the Pegasus manages to hold its own against -three- Cylon Base Stars long enough to get its FTL drives back online. The railguns on the Pegasus seem deadly at close range (And the Galactica too, though its stand-off capability is again worse) as only a couple volley's to the central axis of a base star sent the ship limping away, and as the Pegasus fled we could see it being enveloped in flames.
It appears in the new series the Battlestars excel in close broad-side actions against enemy ships with their large amounts of rail gun battery's while the cylon basestar's are deadly at long range's with uncountable missile batteries and hundred's of raiders at their disposal.