There were many kinds of small combatants, and I wil just give figures for a few major classes. The large Raven and Auk-class minesweepers were originally built with two 3in/50 anmd four .50s. By 1944 they had eight 20mm in place of the 50s; in some ships one of the 3-inchers was eventually replaced by two 40s. The wartime Admirable-class minesweepers and the 180-feet PCEs, built on the same hull, had a standard armament by the end of the war of one 3in/50, three twin 40s, and four 20mm--extremely respectable for a ship of this kind. The smaller 173 ft PCs originally had two 3-inch/50; eventually the after 3-inch was replaced in most ships by a single 40mm. Some completed with .30 cal, but these eventually were replaced by two or three 20mm. The 110 ft SCs (subchasers) by 1944 had one 3in/50, one 40mm, and three 20s. PT boats originally they had two twin 50s. Many later got one 40mm and one Army-type 37mm. In some single 20mms replaced the twin .50s. There were many variations beyond this. I won't try to get into all the amphibious types, but to cite two of the more important ones: The standard armament of LSTs late in the war was seven 40mm and twelve 20mm; they were scheduled to get 12-40mm, 12-20mm. LCIs usually had four 20s.
There were countless classes of auxiliaries and I'll only mention a few. Mid-war figures are hard to come by, and most of these are for late-war configurations. USN auxiliaries were quite well-armed by the middle to latter part of the war. The Haskell-class transports (Victory ships), for example, had one 5in/38, 12-40mm, and 10-20mm. Other transports were even better armed. The General Squier (C4) class had four 5in/38, 4-40mm, and fifteen twin 20mm. A more modest auxiliary, the Liberty ship AKs (cargo ships) of the Crater class, had two armament variations: one 5in/38, one 3in/50, two 40mm, and six 20mm; or one 5-inch, four 40mm, and twelve 20mm.
The armament of the big fleet oilers is well discussed in Wildenberg's "Gray Steel and Black Oil." The first three ships of the Cimarron class (a naval variant of the Maritime Commission T3 tanker) completed in 1939-1941 with a remarkable armament of four 5in/38 with a Mk 37 director, as well as four .50s. Later ships of this class, at least to mid-1943, got a more modest main armament of one 5-inch, without Mk 37, and four 3in/50. Light AA in the big oilers by later 1942 included two quad 1.1s and six 20mm. Beginning in 1944 40mm guns replaced the 1.1. By December 1944, standard armament in the Ashtabula class (T3) was one 5in/38, four 3in/50, four 40mm, and eight 20mm.
Again, just a small sample, with figures from Robert L. Scheina's "U.S. Coast Guard Cutters & Craft of World War II." The most famous cutters of the war were the 327-foot Treasury class. They completed in 1936-1937 with two 5in/51, two 6pdr, and one 1 pdr. By 1940-1941 most had two or three 3in/50, and some at least got a third 5in/51; ASW equipment was fitted about this time as well. Late in the war most operated as amphibious force flagships. In 1945 most had two 5in/38, three twin 40mm, and 4 to 8-20mm. Taney, though, had four 5in/38, while Duane had fourteen 40mm. The 165-foot Escanaba class completed in the mid-thirties with two 3in/50. By 1942 most had in addition two single 20s. This seems pretty light, although Scheina does not mention any subsequent modifications. The 255-foot Owasco class, which began appearing at the very end of the war, had a quite formidable armament of two twin 5in/38, two quad 40mm, and four 20mm.
The armament of merchant ships varied considerably, and like that of warships increased substantially in the course of the war, to a fairly impressive level. Early in the war ships had whatever guns could be scraped up; a ship might have a 4-inch gun and two .50s. Liberty ship Stephen Hopkins, at the time of her famous duel with German raiders Stier and Tannenfels in September 1942, had one 4-inch gun, two 37mm AA, and six machine guns (presumably .50s, but maybe .30s). Later in the war, though, the closest thing to a standard armament for a U.S. freighter was one 5-inch aft (5in/38, 5in/51, and maybe some 5in/25s), one 3in/50 forward, and eight 20mm. [Justin F. Gleichauf, "Unsung Sailors: The Naval Armed Guard in World War II]. To give one example: Liberty ship John W. Brown, now preserved in Baltimore, was completed in 1942 with one 5in/51 aft, two 3in/50 forward, and four 20mm--pretty good for a merchantman at that stageof the war. Later she had one 5in/51, three 3in/50, and eight 20mm. [Sherod Cooper, "Liberty Ship: The Voyages of the John W. Brown, 1942-1946"] Tankers generally were larger and more valuable than freighters, and I suspect had a heavier armament. I cannot find armament figures for merchant tankers, however. (Sawyer and Mitchell's books are the major authority on World War II standard merchant ships, but they seem to have regarded armament as extraneous to the ships and did not discuss it; "Victory Ships and Tankers" has no details on the armament of the standard T2 and T3 tankers, as far as I can tell.)