Honshu shuttlecraft
The Honshu shuttlecraft was a Type 6 shuttlecraft assigned to the  in 2374.

This shuttle piloted from the Honshu by Dukat and Sisko, before the starship's destruction following an attack by Cardassian destroyers. The shuttle was taken to a planetoid and later stolen by Dukat. ()

Dukat used this shuttle to remain mobile for the next few months while he immersed himself in the study of the Bajoran Ancient Texts. He learned of a Bajoran artifact in the Cardassian Central Archives that contained a Pah-wraith, which he thought could be used to make the Bajoran wormhole safe for Dominion ships to travel through. He used this shuttle to travel to Cardassia Prime and to Deep Space 9 while enacting his plan. Before leaving Cardassia, this shuttle was outfitted with a Dominion transporter. ()

Background information 
The interior of the shuttlecraft was used as a backdrop for Dukat's appearances in "Wrongs Darker Than Death or Night" and "Tears of the Prophets". The Dominion transporter effect was used when Dukat beam into and out of DS9 in the latter episode.

Dukat could still have been using this shuttle in , since he beamed out from Empok Nor at the end of that episode using a Dominion transporter, and , since it was never established how Dukat made his way to Cardassia. Since Dukat leaves Cardassia in disguise with new travel documents and identification papers provided by Damar, it's unlikely Dukat would have used this shuttle to travel to DS9 in .
Unnamed Federation shuttles