In my recent post about the 'right' (meaning: efficient and effective) way to clean a toilet, I mentioned those often nasty things that hold the toilet bowl securely to the floor. It seems they're so often pretty gross looking, with suspicious gunk (or crud, if you prefer) around them. Assuming that your toilet isn't leaking, this stuff is just ugly and can be removed. All you need is a spackle knife (NO! Do not use a kitchen or table knife!), a ChoreBoy or Brillo pad and some clear caulk.
Take that plastic cap off, and you'll find a simple bolt with a nut. You should check to see that the nut is secure. With a pair of pliers, give it a twist. You're not trying to actually 'tighten' it unless it's actually loose. Just checking.
Next, with your spackle knife, scrape away old, discolored caulk. Then, with your damp Brillo pad, gently scrub away the remaining caulk residue. You can't always get every last bit of it, but get as much as you reasonably can. Dry the area thoroughly. Clean the plastic cap, and dry it, too.
Now, squeeze a little 'bead' of clear caulk around the edge of the plastic cap. A toothpick or similar will help you push it around. Press the cap back into place with gentle pressure. Leave it alone for at least 24 hours so the caulk can dry and you'll have a nice looking bolt area and seal.