So what are the limits. My first run i just went to the mage college and didnt bother with the war. But as far as that goes, what guilds can i join and still be eligable to join another, or what ones nix me from joining an other...?

For example lets say i want to join the Companions would that mean i couldnt join the blades or whatever, like if i joined the brotherhood would that make me not able to join the empire?

I think you can mix and match as much as you want. I haven't started the civil war quest line at the moment so I don't know about those two but I'm the Arch-Mage of the College of Winterhold as well as a member of the Companions, the Thieves guild and the Dark Brotherhood at the moment.

I'd put money on the side you take for the civil war quest line not being affected by your other guild choices.

I think you can do everything. I'm a full blown mage and I'm currently doing the companions and the college. And I'm going to to the stormcloaks and then I will go from there to the other ones!

The only one is that if you pick one side in the civil war you cannot do the other. (Obviously!)

i have finished Companions, Mage college, Dark Brotherhood and the thieves guild in one run.. still not done with that playthrough (even though i have finished the main story, and also helped the imperials in the war)