Okay, so I've been playing Runescape since 2001, at the end of it's first year of operation. It wasn't until May of 2010 that I started playing World of Warcraft, and I have to say that the games are heavily incomparable.
Runescape is a game that heavily focuses story-driven quests, co-operative activities, and level-based character advancement. PVP is an aspect of Runescape, but it's definitely not a core aspect. The skills are diverse and all have very unique mechanics that set them apart from the other skills.
Now World of Warcraft focuses on smaller quests. There may be stories within the quests, but most of them are very simple and lack any of the depth that Runescape quests have. The co-operative activities are pretty much limited to Dungeons, Raiding, and team PVP which, while they're all great fun, lack the diversity that the various Runescape activities have. The controls of WoW are customizable, manageable, and intuitive, but they're not at all original to WoW. These sorts of controls have been prevalent since the early days of EverQuest. That said, level advancement in WoW is only the simplest part of gameplay, and for most players the game doesn't even really start until you hit the max level. For that purpose, character advancement is much heavily focused on gear-advancement, rather than levels. PVP is an immense part of WoW's gameplay, and makes up for much of the end-game content.
So which game is better? That's really up to the player. Some people suggest that Runescape's lack of limiting people based on a class make it better, but anyone who's played through WoW knows that the reason classes exist is because each individual class is so comprehensive and unique that if the game were completely open-ended, the complexity would be impossible to digest. Similarly, people criticize Runescape's inferior graphics but when viewed in perspective (considering that Runescape runs entirely in the browser on a Java engine, rather than Blizzard's standalone platform) the graphics are probably comparable to one another, as WoW's graphics, while being more visually pleasing that Runescape's, aren't necessarily that amazing by modern gaming standards.
My vote personally goes to WoW, but that's just because I enjoy it more and it caters more to my style of gaming. The butting of heads in this thread just proves that the games are on par with one another, and people just prefer one over the other because the games really call for a much more diverse still of gaming than the other.