Well in most cases your only using 0.05% one half of one persent or one drop in a 10ml solution. In some cases you'll use two drops or 1%. "Real Lemon" juice, the stuff you can buy at any grocery store, is only used to bring out the fruit flavors in your mixes. I would not recomend you try to use it as a flavoring. Trust me on this one, I've done it. It tasts great dripping it onto your finger, but once the coil heats it up it looses it's lemon flavor and tast burnt. Nasty!
So if your looking for a lemon flavoring to flavor a juice then get one from LorAnn, TPA, or any of the other "flavoring" vendors. If your looking to "inhance" other flavors then go ahead and try a drop or two of the "Real Lemon" lemon juice.
I don't have any experance as far as limes go, but I would assume it would be the same.
If you do use fresh squeezed juice I would filter it before putting it in a mix.
At 2 drops (per 10ml) it doesn't really change the color all that much. Might add just a hint of a transparent yellow hew to a clear mix if you look close but I wouldn't worry about that.