Caulking around base of toilet
Two words: clear silicone. 

You can match any toilet to any floor effortlessly if you use the clear stuff. It transmits the colors of the toilet and the floor and doesn't create an ugly, wavy visual line. 

I usually use a finger if I'm dealing with a larger gap. Silicone wipes off skin cleanly enough that it's not a problem. Try to fill the void fairly flatly so you're not pulling a lot of caulk along as you tool it out. Err on the side of too little. 

Note: While I don't agree that toilets should be left completely uncaulked to show failure of the wax ring seal, I do think it's wise to leave the back portion open for that reason. It's often difficult to reach that area with a caulking gun anyway.