I hesitate to get into this discussion. I've been building ship models for - well, let's not get into how many years, but I've only seen a fraction of the kits available. I haven't been buying many in the past few years, and I know I've missed some good ones. There's no well-stocked (for ship enthusiasts) hobby shop near where I live, so I haven't had the chance to look at many newer kits in the boxes. I haven't kept up with all the superb warships from Dragon, for instance, and I haven't seen anywhere near all the Trumpeter ones. I know Revell Germany has brought out several fine kits in recent years, but I can't claim to have seen more than a few of them. And I've never laid eyes on a Zvezda ship kit. (Mr. Stauffer listed the Revell Emden and the Zvezda Dreadnought, for instance; I know from reviews and photos that they're excellent kits, but I haven't actually seen either of them.) There was a time when I routinely bought new kits and put them in my considerable stash, but those days are gone; I can't lay out $100 on a kit that I may build someday.
With those caveats, here are 20 plastic kits that are among the best I'm personally familiar with:
Revell 1/96 Constitution
Heller 1/100 Victory
Airfix Wasa (I haven't seen the Revell one)
Heller La Reale
Revell Viking ship
Revell Golden Hind
Revell Mayflower (both scales)
Revell Charles W. Morgan
Dragon 1/350 Buchanan (and sisters)
Trumpeter 1/700 North Carolina and Washington
Trumpeter 1/700 Queen Elizabeth
Dragon 1/700 Essex-class carriers
Dragon Bismarck
Dragon 1/700 Arizona
Imai 1/125 Cutty Sark
Revell Flying Cloud
Tamiya 1/700 Yamato
Tamiya 1/700 Missouri (and sisters)
Trumpeter 1/700 Saratoga
Sealsmodel 1700 Mikasa (I haven't seen the 1350 Hasegawa one)
I haven't included any wood kits (because the quality of a finished one depends so much on the modeler rather than the kit), or resin ones (because I don't have much experience with them; I'll leave them to somebody else).
I'm sure dozens of other styrene kits belong on the list. I know quite a few from Dragon, Tamiya, Hasegawa, Trumpeter, Zvezda, and Revell Germany by reputation, but I have no personal experience with them - or, in most cases, the funds to buy them. (To build the Hasegawa Akagi, with all the manufacturer's photo-etched detail sets, would cost close to $700. To me, at least, that's not pocket money.)
Those 20 are just the ones I happen to know about - and can recommend with few, if any, reservations. I reserve the right to add more when and if I think of them.