For me I'd say that the greatest RTS out of the box would be Total Annihilation (1997) with both of it's expansion packs. The game has literally hundreds of units that are unique to each faction, there are dozens of multiplayer maps, the campaigns are enjoyable, and it has a stellar soundtrack
. Unfortunately Total Annihilation lacks in customization. There are lots of user made maps, mods, and custom units, but there is no built-in map editor like in most other RTS games, and there are no custom games like in StarCraft or other RTS games, there is only melee in Total Annihilation (destroy your enemies base and kill his/her commander). Another shortcoming of Total Annihilation is that when you head online, unlike StarCraft: Brood War, it can be relatively hard to find people to play with. You can however find a few people on PhoeniX WorX, WarZone, and GameSpy Arcade however.
However, for a game that has been perfected, I'd say the original StarCraft (1998), with Brood War. StarCraft has a great storyline, unique units for each faction, a built in map editor, an average soundtrack, and the greatest online service of all time, the original (not 2.0) Battle.net. One thing that separates StarCraft: Brood War from the hundreds of other RTS games out there is not only Battle.net, but the ability to play custom games on Battle.net. The original map editor was pretty weak, but the community created several custom map editors (I recommend X-tra Editor in special mode for units and triggers, and StarForge for terrain) to create maps with. Custom maps range from defense maps to RPGs to bounds to movie maps to zombie survival maps, and everything in between. StarCraft also has millions of players from all around the world and is still the most popular RTS game of all time, despite being over 10 years old.