There are all sorts of options on the market, from squeeze tubes to power caulk guns. For the average homeowner I recommend a standard caulk gun. It's inexpensive, easy to control and gets the job done.
A common mistake is cutting the tip of the tube too far up so that the bead comes out in a big, thick blob. Make sure you only cut the tip as wide as the gap you're trying to fill. This way you won't have to deal with excess caulk.
If you cut the tip at an angle and then apply the bead of caulk so that the tip of the angle is at the top of the bead it will smooth itself out as you work and leave you with a perfect finish.
If you're not that adept with a caulk gun, don't worry. One of the best tools you can use is your own finger. Dip it in some cool water and then smooth over the bead. It molds to the surface and you have more control over your finger than you would another tool.
After each pass, wipe your finger with a wet cloth. If not, it's going to get gummy and mix with the oils in your skin leaving a residue behind on the next bead you smooth.
It may seem obvious, but when you're laying down a bead of caulk, make sure you release the trigger as soon as you finish, if you don't you'll have a bigger mess.
Once you're finished, if there is any caulk left in the tube, release the pressure by turning the bar on the back of the caulk gun and then remove the tube.
Seal the tube with an electrical nut to keep it from drying out. I'm Mrs. Fixit and it's just that simple!
