According to the show's producer and senior writer, Joseph Mallozzi, the floor lines have no particular in-universe meaning and were evidently just set dressing, presumably to add a little bit of background colour to sets that would otherwise have been various shades of grey and brown.
Q. Did the lines have any actual behind-the-scenes meaning? Or just decoration?
JM: Nope. To the best of my knowledge, no special meaning.
As pointed out in another answer, these are presumably queue lines, allowing people to be directed verbally to a particular location.
Interestingly, courtesy of an auction of set blueprints where the lines are visible, and the cleaned-up SGC floor plans from Richard Dean Anderson and Joseph Malozzi's official websites, we can actually map where the various colours go.
The lines travel from the main elevator into the complex. The blue line leads to the Secondary Elevator, the green on the right leads to the Stair (to Level 28), the red line leads to the Primary Gateroom Entrance and the green line in the middle leads to the Infirmary.