Class-D Nuclear Warheads are considerably more compact than any nuclear device currently known and qualify as a "suitcase nuke". Judging by the total instant destruction of the Cylon Basestar in Kobol's Last Gleaming, they would appear to have a yield in the megaton range.
The exact technical details are not revealed in the series, in keeping with its philosophy of avoiding technobabble. However Probably a Class-D Nuclear Warhead is a fission-fusion bomb with a very high efficiency of matter to energy conversion. Given the small size of the device that Baltar delivered to Gina, the fissile core is extremely small, and the the apparatus which compresses it to supercritical mass is equally compact. By itself the fission primary has a very low yield for a nuclear weapon; possibly only into the range of very large conventional bombs. In a fully assembled Class D the fission primary is used to ignite a fusion reaction which creates the vast majority of the yield.
From its small size it seems likely that a nucleide other than plutonium is used in the fission primary. Aside from the rather unscientific introduction of a "new element", the most logical candidate would be Californium. This synthetic element exists only in miligram quantities in the real world, but the Colonies might produce much more using advanced -- but plausible -- technology. Cf-251 has a critical mass of around two kilograms, and this could be reduced even further using currently existing techniques. The Class D warhead is advanced technology, but it is in no way physically impossible, nor must it rely on scientific principles unknown in the present day.
Notes
- This article is assuming that the shown nuclear warheads are Class D.
- In the United States military, Class-D is the designation of a light-weight Thermonuclear weapon. The W-28 warhead in the B-28 TN bomb is an example of this type.