So, in the past I'v heard rumors that if you play the same game, on different systems there will be differences in content (usually small) I'v never confirmed this before. But it is one of my concerns. Is this true? Will possibly an item,quest,etc from a game on one system, be missing on another system?

Has this ever happened in an ES game?

I don't see any reason why this would happen. But since I cannot confirm or refute this idea, I figure I would ask.

When they say "content" they usually mean "graphics". To me that's a moot point and doesn't even matter, but some people get up in arms if it doesn't have 32x AA and ultra high resolution uncompressed png textures and billion polygons in the hand. Very rarely where there be actual content differences between platforms, and those are usually underhanded DLC type pre-order bonuses more often than anything else.

With a few exceptions:

Sometimes a PC version of the same game will allow more players in co-op, and sometimes the 360 version will have more zombies on the screen at a time than the Wii version. That's really the only two examples I can think of. Everything else is graphics.

Bethesda games have all been pretty level across the platforms with almost no differences. Besides mods, which Bethesda has no control over anyways, Morrowind and Oblivion (and Fallout 3) were the same exact game on every platform you found it on. The only thing now is that Skyrim on the 360 will get DLC a few months before the PS3 and PC because of underhanded business tactics.

The hardware in current generation consoles is getting a bit dated. No current gen consoles can even run true 1080 resolutions, they have to render it at 720p and then upscale. Modern gaming PCs however are much more powerful which means that they can display more stuff on the screen at the same time and render everything at a higher resolution. Basically what Steampunk said.

The console versions of games usually have the same content (Quests, Items, such things) as the PC version, but they may not have the same content (here content means graphical assets such as textures and models).

http://en.wikipedia.org/wiki/Soul_Calibur_2#Ports