Clean tones are often considered to be produced only when your guitar is running directly to your amplifier with no effects between. However, there are a variety of effects you can use to create interesting sounds. Chorus pedals simply repeat the notes you are playing at close intervals. This helps to create a thicker, fuller sound. Kurt Cobain of Nirvana used a vintage Polychorus pedal on "Come As You Are," and Slash of Guns N' Roses used a chorus pedal extensively on many songs through the 1980s, including a cover of Bob Dylan's "Knocking On Heaven's Door."
Overdrive and distortion are perhaps the two most commonly used effects by guitar players. Overdrive is achieved when the gain of an amplifier is turned up to the point that the internal circuitry of the amplifier cannot handle the volume. This will not damage the guitar amplifier, but it does create overdrive. The difference between overdrive and distortion is small--- distortion is simply a more intense version of overdrive created by using more input gain.
Many effects pedals simulate this sound, and they are often used in situations where maximum guitar amplifier volume is not possible. Musicians who perform live tend to find it difficult to alternate between clean and distorted sections of a song without the use of an external overdrive or distortion pedal.
Many guitarists use one or more equalizers to help shape and change their guitar sound. Equalizers allow you to adjust the frequencies made by your guitar. An equalizer set to remove very low frequencies and very high frequencies would be ideal for rhythm guitar. An equalizer set to accentuate mid-range and high frequencies would commonly be used for lead guitar or a guitar solo. Several equalizers can be used in the same effects chain to minimize the time spent switching between tones, which may not even be possible in a live setting.
Reverb and delay are commonly used time-based effects. Many amplifiers have reverb controls, and there are numerous external effects pedals that create reverb. Reverberation can help accentuate many different playing styles for both rhythm and lead guitar. Delay is similar to reverb because they both create a series of echoes, but delay pedals create a distinction between echoes, while reverb blends those echoes together. Delay pedals are frequently used for both rhythm- and lead-guitar sounds.