I did find this after doing some more research.http://www.varesano.net/blog/fabio/how-disable-internal-arduino-atmega-pullups-sda-and-scl-i2c-bus
I'm still pretty new to all this, but what it sounds like to me is that you really only want one set of pull-up resistors on the I2c buss.
From here it states that if you are using the data logger shield, it has another set of 5v pullups on the built in RTC.http://forums.adafruit.com/viewtopic.php?f=31&p=117658
And the BMP085 already has some pull up resistors on it's PCB.
So, my guess here is that since I was using the ethernet arduino with the built in micro SD and the add on RTC, I was still at risk.
but if I disable the built in pullups on the i2c buss I should be able to use the DS1307 and the BMP085 just fine?
(I could be very wrong on all of this).
Now my only question is what will happen if I add something else?.
I think it's probably just going to be safer if I don't mix the DS1307 into the I2c buss and go down the path of seeing what it will take to put it on its own set of pins. (Which is what Ado suggests).
Just part of the fun figuring things out I reckon, as long as the magic smoke doesn't come out of anything...