Do you mean the lines between the panels or the panels themselves? Some people do weather individual panels, but I suspect you mean the lines between the panels.
I use artist's water colors or artist's acrylics (note that these are not the chalky kid's water colors nor the acrylics we normally paint models with). Thin either one with a lot of water and a couple of drops of dishwashing detergent. Use a thin, pointed brush, dip it in the soup and touch it to the panel line and it should run right down it. If not add another drop of soap. Use a moist Q-Tip to remove any excess that gets outside the panel line by rubbing ACROSS the line, not along it.
IMPORTANT! For this to work properly the model MUST have a smooth finish (which is normal since decals need a smooth finish as well). If the finish is flat you'll have a terrible time getting the excess off. If you need a flat finish shoot it with clear acrylic flat when you are finished.
For more details, check out Swanny's instructions at:
http://www.swannysmodels.com/Weathering.html