I find I have difficulty narrowing down my favorite choice.
Top 5 in no specific order:
Legacy-Class
Defiant-Class
Intrepid-Class
Stargate's "Atlantis" City Ship.
Atlantis' Puddlejumpers.
I'm just not a fan of the Destiny as its fracking extraordinarily large, as I haven't seen any indication it was used to manufacture / drop spacegates or regular stargates as part of its original mission during the Ancients' expansion into the universe, pre-Wraith/pre-Replicators.