The Big Three Progressions 

How does one decipher the chord changes of a standard? The most obvious sign to look for is the II-V-I progression in the home key, which just about every standard tune will contain.  But of course, most standards contain other chords and, at first glance, it can sometimes seem that the composer or arranger just threw in a bunch of chords haphazardly. However, most standards aren't just random chords thrown together when there isn't an obvious II-V-I. Many standards modulate to different keys, so this would be one of the first things to look for (in other words, figure out the key of the tune, figure out where the II-V-Is happen in that key, then figure out where all the II-V-Is in other keys happen. Keep in mind that a II-V sometimes happens without the I.) Other diatonic chords such as the IV or VI chords are also sometimes used.

For example, the first four bars of "All the Things You Are":
| Fm7 | Bbm7 | Eb7 | Abmaj7 | Dbmaj7 |
This progression contains a II-V-I in Ab and is flanked on either side by the VI and the IV chords in that key. 

The next three bars contain a II-V-I in a completely new key, C:
| Dm7 G7 | Cmaj7 | Cmaj7 | 

Also, don't forget minor II-V-Is, where the II is usually a half diminished chord and the I, of course, is minor. A tune like "Autumn Leaves" goes back and forth between major and relative minor (minor key built from the VI chord in the major key):
| Am7 | D7 | Gmaj7 | Cmaj7 |
| F#m7b5 | B7b9 | Em7 | Em7 |
Here, the first three bars are a II-V-I in G, the fourth bar is the IV chord in G, and the next 4 bars are a II-V-I in E minor, the relative minor of G major. 

Just this material covers a pretty large percentage of what you'll run into in standards, which is basically a V-I progression, usually embellished by the addition of the II chord before the V (and further embellishment by the occasional addition of other diatonic chords). 

One other note:
Don't forget diatonic 3rd substitution where a chord is substituted for a chord a 3rd away. Probably the most common use of this substitution is when the III minor7 chord is substituted for the I major 7. 

The basic idea behind harmony, music in general, and art in general (and I guess life and the universe in general), is dissonance to consonance or conflict to resolution. A scientist might say something like energy dissipates to a state of rest. Anyway, V to I is the main way this is accomplished in the harmony of most standards but not the only way. I've found that, along with V-I, two other progressions pretty much cover all the harmonic bases in the vast majority of standards. 

The second most common progression is minor IV to I. In the key of C, this would be F minor to C major. Obviously, F minor isn't diatonic to the key of C, so we need some other scale to justify its existence. If we look at the possible minor scales, such as natural minor, Dorian, Phrygian, harmonic and melodic minor, it's apparent that F melodic minor (F, G, Ab, Bb, C, D, E) has the least number of notes different than C major (C, D, E, F, G, A, B) of all the F minor scales. The fourth mode of F melodic minor is Bb Lydian dominant. If you build a chord from the fourth scale degree, you get Bb, D, F, Ab (which forms a dominant seventh chord) and the upper extensions of C, E, and G (9th, #11th, and 13th). This chord is a common substitute for the minor IV (F minor in this case), so the progression could be represented by:
| Bb7#11 | Cmaj7 | 

Notice that "#11" is specified in the chord symbol of Bb7. In many cases, you won't see that extension specified, but using it does make it more clear that you are specifying the minor IV to I sound of F melodic minor to C major. 

An example of this progression would be this passage from "My Romance" (bars 9-12):
| Ebmaj7 Ab7#11 | Bbmaj7 Bb7 | Ebmaj7 Ab7#11 | Bbmaj7 |
The tune is in Bb, so this example starts with a IV chord, Ebmaj7. Then we have Ab7(#11) which is a substitute for Eb minor, for which the logical scale would be Eb melodic minor.
In bars 10 and 11 we see a V-I in Eb. The use of the Bb7 is called a secondary dominant.  A secondary dominant is a V-I (or II-V-I) in a key other than the home key where the resolution chord is one of the other diatonic chords from the home key.  In the example above, the Bb7 would usually be referred to as "V of IV."  Other secondary dominants would be V of II, V of V, and so forth.

The third of the "big three" progressions is I diminished seventh to I major. In C, this would be:
| Cdim7 | Cmaj7 |
This progression is also usually represented in a jazz context "in disguise." Most people who know even a little about theory know that a diminished seventh chord is a symmetrical structure built in thirds and that you can play any voicing for a diminished seventh chord up and down in minor thirds (every three frets) to get different inversions of the chord. One of the inversions of C diminished would be Eb diminished. Next, go back to the "diatonic third substitution" idea and substitute E minor for C major. Our example would then become:
| Ebdim7 | Em7 | 

It's pretty common to see a progression like this:
| Cmaj7 | Dmin7 | Ebdim7 | Em7 |
There are a couple of interesting things about this progression. The first is that resolution to the I chord is sometimes delayed or even combined with another progression before the resolution to the I chord. This progression is a common one:
| Em7 | Ebdim7 | Dm7 | G7 | Cmaj7 |
Here, the I diminished to I major (Ebdim7 and Cmaj7) is separated by a II-V (Dm7 to G7). It's a double resolution; I diminished to I and II-V-I. Notice, also, that the progression looks like a backwards version of the previous example. The second interesting thing about this progression has to do with the diminished chord and its scale. The whole-half diminished scale is typically thought of as the diatonic scale for a diminished chord, and the half-whole diminished scale is typically thought of as the diatonic scale for a dominant seventh chord with a flat 9 and a natural 13. The two scales and chords are very closely related. For example, play a C diminished seventh and then put a B in the bass, and you have a voicing for B7(b9). 

This substitution is often used in a I diminished to I major progression, especially when the I major is replaced with the IIIm7. In C this would be:
| B7b9 | Em7 |
instead of:
| Cdim7 | Cmaj7 | 

Also, the dominant 7th chord is often preceded by a half diminished chord a fifth higher to form a minor II-V:
| F#m7b5 B7b9 | Em7 | 

An example of this progression can be seen in the last eight bars of "Green Dolphin Street":
| Dm7 | Bm7b5 E7b9 | Am7 | F#m7b5 B7b9 |
| Em7 A7b9 | Dm7 G7 | Cmaj7 | Cmaj7 | 

Here, the B7b9 to Em7 is a sub for C dim7 to C maj. 

So, to recap, my theory is that you can play jazz/bebop with three different progressions:
V-I (usually written as II-V-I, sometimes just V-I, sometimes just II-V, and sometimes with other major diatonic chords thrown in) 
IV min-I (usually written as bVII7 to I, using the melodic minor from the IV as the "upper structure" to the bVII) 
Idim7-Imaj7 (usually written as bIIIdim7 to IIIm7, or VII7b9 to IIIm7—doesn't always resolve directly to the I chord.) 

Although I'm attempting to simplify the basic jazz harmony that's used in typical standard progressions, all of this material may seem overwhelming to someone just getting his or her feet wet with jazz improvisation. My suggestion is that, whatever you're working on, just try practicing it very slowly. And you can also break it up into small sections; just try looping four bars over and over again really slowly. I also recommend, when you do something like this, try restricting yourself to only one string or only one position (within reason; within two or three frets). 

As an example, let's elaborate elaborate on the tune "On Green Dolphin Street." Those last eight bars are the toughest part, but it really only boils down to a few key centers:
| Dm7 Dm7/C | Bm7b5 E7b9 | Am7 Am7/G | F#m7b5 B7b9 |
| Em7 A7b9 | Dm7 G7 | Cmaj7 | G7 ||
The first bar is one of those II V's that doesn't resolve to the one (or in this case, even the V; you could say that it eventually resolves to the V several bars later) so, here, the key is C.
The second and third bars are a II V I in A minor, the relative minor of C. Lots of people play different things over minor II V's, but I've always thought that the harmonic minor scale worked the best as sort of a basic minor key scale; I think of other sounds as substitutions for the harmonic minor. Note that even this theory isn't airtight; with the harmonic minor scale, you have a natural 7th (G#). In order to use Am7, which is common-practice on a minor I chord, you need G natural for the flat 7. Notice, though, that as long as you don't really lay into the G# over this chord, and treat it as a resolve tone to A, it works just fine. 

We've already covered the F#m7(b5) to B7(b9) (C diminished scale), which resolves to the Em7, a substitute for Cmaj7. 

Lastly, there's a typical III-VI-II-V-I progression. The A7(b9) functions as a secondary dominant to Dm7, the II chord, so for those two beats, we're in D minor, which, based on the previous logic, would be the D harmonic minor scale. The II-V-I (as well as the V to get you back to the top of the form for the next chorus) are all in C. So going strictly by key centers, the last eight bars of the tune would look something like this: | Cmajor | A harm min | A harm min | C dim |
| C major D harm min | D harm min C maj | C maj | C maj || 

Keep in mind that we're talking about key centers only here.  If you practice the above scales furiously until you can play them up and down and switch keys at the right time, that's only a small part of the puzzle.  It's also important to be able to arpeggiate the chords and to voice-lead from chord to chord when improvising, but this goes beyond the scope of this article.  Also, in actual practice, many jazz players would embellish this basic structure with extra substitute harmonies. Some obvious examples might include using the altered scale (7th mode of melodic minor), or half whole diminished scale over the V chords (E7(b9), for example), or catching the F#m7(b5) chord by using the Locrian natural 2 scale (6th mode of A melodic minor) for those two beats before going to the C diminished (which is really the same scale as B half-whole diminished, which you could use if you were strictly thinking of these two chords as a II-V in E minor). 

Another interesting point worth mentioning is that I've noticed, to varying degrees, that the longer I play, the more it seems that the "big 3" progressions seem to be somewhat interchangeable. For example, if I see:
| Dm7 | G7 | Cmaj7 | Cmaj7 |
I often stick in one of the other two progressions and it works just fine:
| Dm7 | Bb7(#11 )| Cmaj7 | Cmaj7 |
| Dm7 | Cdim | Cmaj7 | Cmaj7 |
or actually, here's a common one that a lot of people use:
| Dm7 | G7 | C dim | Cmaj7 |
In this case, the II-V is intact, but the resolution is delayed by a bar and you have a double resolution—both II-V-I and I dim - I maj.