I am really green with phase issue but I have started digging into them take a look at the picture link are these wave files in phase or out?  They are a sax recording one wave is of the body of the sax the other is a wave of the bell.  Still not sure what out of phase looks like but my vote is these are out of phase http://i242.photobucket.com/albums/ff157/bmog76/Phase.png 

Zoomed in that far, you can readily see the delay between the two signal paths. This will cause phasing issues, but cannot lead to a true "out of phase" scenario where they can null each other out (also because they are not identical, such is impossible). You should be able to zoom in similarly on the beginning of each wav and align (nudge) the first obvious transient to mate them better, but the area in the picture is unclear of which transient is delayed (and by how much).

Since the sax will not be bolted down there will be constant but minor changes in the phase as the player performs  (movements due to breathing, finger changes, swaying as it's played, etc.).
 
Trying flipping the phase on one of the mics and go with whatever sounds the best.
 
Personally I never had a phase problem recording sax but I never used 2 close mics.
Usually I used a combination of a dynamic and a large diaphragm condenser.
I usually had the dynamic 2" to 6" from the sax aimed down the bell (favorite was an RE20) and the other a foot to several feet away (usually something like a 414, C12a or u47) - distance depending on the musician and the room.
These were mixed live to one track (2" tape era).
Exactly where the condenser was aimed depended on the instrument - with clicky pads or noisy keys aiming directly at the body of the sax could capture a lot of noises distracting to the performance.

I agree with mettelus with this. They are just two different waveforms and when added might give you a slightly different sound. A true out of phase waveform would be more like one waveform being totally inverted to the other which this is not.
 
I also agree with TheSteven in that it is not necessary to use two mics either. You could just be asking for trouble.  Most of the sound is in or comes from the bell and I have always got a great sax sound by putting a decent mic near the bell.  If one mic will do the job then use one mic.  It saves you a lot of hassle later on.
 
In this case I would just use the bell sound only and leave the other off.  The body tends to pick up a lot of unwanted noise at the end of the day too.
 
If it is a world class sax player recording you will get the sound and the take will be brilliant and that is all that matters really.

Another option for recording a sax is a single mic around three or four feet away pointed roughly at the middle of the instrument, about where a seated listener's ears would be. Captures the sound as a listener would hear it, and no multi-microphone phasing issues. Helps to keep the pad and mechanism noises that close mics pick up so well down as well.

Waves InPhase is good at tackling slight out of phase issues. Expensive at full price, but like most things Waves turns up heavily discounted in a sale quite often.

Another option for recording a sax is a single mic around three or four feet away pointed roughly at the middle of the instrument, about where a seated listener's ears would be. Captures the sound as a listener would hear it, and no multi-microphone phasing issues.

 
This is my preferred method.  The bell is loud, but contains quite a bit of trash as well.  The instrument resonates through its entire body and a great sound come from the entire instrument, not just one part.  Pointing the mic at the players mouth is also a good technique to keep the instrument slightly off axis, which tames quite a bit of the high frequency noise.  Be sure the player does not move much in any case.  I have noticed everything from uneven levels to Doppler shift with visually dynamic players.  
 
 

Since you are looking at two different instrument wave forms, I doubt seriously that you would have a phase issue between them.
 
Phase issues will occur any time you combine 2 waves as we tend to do all the time. It increases dependent on the number of tracks combined or mixed.  You will have additive and subtractive interactions between them all at any given point in time. The big question is, can you hear that phase interaction?  And under most conditions, the answer to that is "no", probably not.

In most cases, the time that phase becomes important and perhaps noticeable is when you have 2 identical or almost identical tracks with a very slight timing difference between them.  Doubled vocals can do this easily.  Even if you record 2 unique tracks of a guitar or a vocal they may be so close that they do present problems with phase. This also exhibits when you are recording one instrument using 2 mics that are at a slightly different distance from the instrument.  Acoustic guitar with 2 mics for neck and body, one close, one a bit further out..... or an amp... one mic close on the speaker and one further back to get the room ambience. Under these conditions, the sound source is identical, but the sound is hitting the mics at a slightly different time, and that, depending on the frequency, will either be in phase, out of phase or at some point in between. We can live quite comfortably with the "in between" area.  Swapping the mic/track phase (playback mode) may be useful in solving the issue or simply moving one mic a few inches could solve it.

Those two waveforms are actually not radically different from one another, they are mostly just out of phase. I'm guessing they sound kinda hollow when blended and sound better when soloed. I'd bet they could be nudged together and you'd only maybe get comb filtering at the upper end of the spectrum. 
 
But I wouldn't bother. I'd just use one microphone and experiment with placement and distance. If the room sounds good, and the sax is recorded solo, the tone will benefit greatly from backing the mike up a bit. Most acoustical instruments do. Although you normally see saxophones close-miked, that's not done for tone, it's for separation.

Say you are recording a modern jazz quartet type of sound eg piano bass drums and sax.  You are aiming for a more close mic modern type of sound.  Putting the sax mix 3 or 4 feet out from the front of it may not work so much and give you the sound you want.
 
I have found success in getting the distance right between the bell and the player and the body of the sax. Even at 12" you can move it into places that are balancing these areas.  It then comes down to the player.  Firstly the tone they create and the horn itself. (every horn sounds different) And then the choice of  Mic and Pre.  As close as I have been at times I have always got a very natural and full and close mic type of sound with minimal noise from the body.
 
Daniel is very right about going too close to the bell because it almost sounds unnatural in there. I am not a fan of the bell clip on mics.  I think they are just too close for starters.  No amount of EQ will sort that out compared to being say 12- 18" away and closer in on the player and the body a little.  Pointing away from the bell a little puts is a little off axis and it can sound nice too.
 
You can still get a beautiful modern natural jazz sax sound and a lot of separation as well from the band.  It's a balance and just needs to be manipulated a bit.
 
Then there is the concept of recording the whole quartet with a stereo mic and in the right room, the right distance away from it and I love it too. Instant great sound from everyone.