For the British, Vosper MTBs and BPB MGBs are a must, so one pack of each. Add another pack of Vospers, if desired, for larger raids, but one will suffice for most scenarios, especially if coupled with the MGBs, in mixed units.
Add in some Fairmile D MTBs, MTB/MGB combo (one had both heavy gun as well as torpedo armament, and is offered in their packs), or MGBs.
The above will work well for the English Channel, and Med.
For Germany, S-170 S-Boats (S-100 class), or their S-26 boats (which are the same as S-38s with the unarmored bridge). Perhaps a pack of each for mid-war, or two packs of the S-170 for the late war.
German R-Boats, VP Boats, MFPs, and AFPs are useful too, along with the occasional Torpedo Boat (really, the German version of a small destroyer).
MTBs and MGBs fought with 4 x VP boughts, off of the French and Dutch Coast, from time to time (dubbed the "Four Horsemen of the Apocalypse), on a number of occasions too.
For both the British and Germans, you can use some of the smaller coasters, tankers, and merchants in the channel. The above mentioned vessels can be used to escort them, and you can add in some larger vessels too, e.g. corvettes, Hunt class DDs, German torpedo boats (for offshore screening of coastal convoys), American Destroyer Escorts, German Destroyers, etc.
Both sides' MTBs and S-Boats ran up against the larger vessels, occasionally.
For the Italians, at least a pack of their MAS 500 class MTBs (can't recall the exact number in their listing – perhaps 532+, or 550+ class). Some of their other boats as well, and corvettes/torpedo boats/destroyer escorts/destroyers, if desired. You can team these up with German MFPs and AFPs too, and S-Boats, since those were used in the Med. Sea also.
For the Americans, I'd go with Elco PTs, but Higgins and others will work too.
For the Japanese, perhaps some barges (can't recall if they make those, or not), or smaller landing craft. Destroyers, destroyer escorts, and other smaller craft too.
The Americans had a number of encounters using MTBs vs. Japanese DDs and larger, so you can definitely do some big game hunting for those.
Throw in the occasional submarine too, for coastal actions, and/or to use for convoy battles, if desired.
Don't forget a few aircraft too, for beating up the vessels, when they get caught out in the daytime. I like using 1/600th scale for those, but you can use the 1/1250th planes too, if desired. Reading a little history will point you in the correct direction for those.
I imagine that should give you a decent start.
Enjoy!
goes to sea with the Terrain Mat.
. What set of rules are you looking at?