The title of the first WC is spelled "WarCraft" (with an uppercase C) in the MG database, but the other games in the series appear to be spelled "Warcraft." SC is spelled "StarCraft." So, which way is it supposed to be?
Looks like an upper case C to me, on all titles. For some reason, though, Blizzard on their site seem to spell it Warcraft with lower case, but StarCraft with upper case.
Looks like it started as a capital "C" and then changed to a lower case "c" later on. The US diskette version has a capital "C" in two different fonts. The 1998 Sold Out release, however, uses a lowercase "c" in the trademark text.
Also StarCraft might need the unusual capitalization to differentiate itself from the aftermarket car part company.
If I had to guess I'd say that they trademarked "Warcraft" thinking it was the same thing as "WarCraft", but it wasn't, so they modified the text over the years to represent what they actually owned. By the time WoW came out it's unambiguously "Warcraft".