This is a guide of when to use which naval units. To see the mechanics and stats of each naval unit, check Naval units
Unit selection
In the start of the game, 
Frigates are the most effective ship in the game. They can hold out during the game due to sheer numbers. Though it may severely lag the game, and crash your computer if you try to look at any battle using 1000 frigates.
Commerce raiders are only better than frigates if one needs a fast fleet. This is because for every one commerce raider you can have, you could instead have 3 frigates.
Large numbers of 
Ironclads are needed to colonize effectively as they award most colonization power, and also happen to be the counter to mass frigates in multiplayer (300 ironclads beats 900 frigates).
Cruisers are the best ship late game. A navy cannot hold with only cruisers though. Building huge cruiser-only fleets means that one will miss when trying to attack dreadnoughts. This means that it is advised to maintain around half of the supply limit being used on dreadnoughts, while trying to balance having a large fleet with having a fleet of powerful ships.
Ships that below par and thus not advised to built are 
Man o' war, Commerce Raider and 
Monitor.
Blockades
Naval blockades can provide up to 25 war score if all provinces are blockaded, the blockade is prolonged and no other battles occur. On top of that blockades also increase the target nation's war exhaustion. They do however only harm the target's economy and trade indirectly (War exhaustion makes factories less profitable).
Blockades do also prevent the enemy from transporting troops over straits, while the blockader can move theirs freely. This can be the key to winning wars in places with a lot of straits e.g. against 
Denmark or 
Atjeh. If troops walk out on an island, it is possible to completely lock them out of the war by blockading the strait.