What is the difference between a Comment and a note ?

A UML Comment:

In MagicDraw UML a «documentation» Comment is a special
case. The documentation of an Element may be displayed or even edited
in a Comment attached to an element by a handle after performing Retrieve Documentation
from the context menu for the attached Comment. Such a «documentation»
Comment DOES NOT appear directly in the model (containment browser).
Visit the following page for an examination of a MagicDraw UML XMI project file to
see how it is stored.

A UML note:

Unless you are using the useful callout feature of a note, I recommend that you use a Comment ! If you don't want to display a Comment's applied stereotype(s) simply switch off the display with the Show Stereotypes options, then it will look like a plain note.

See also:

Comment vs note: where the body text is stored.

A Comment is a true UML model element with a corresponding metaclass. A Comment element - along with it's body text - is stored in the model's "repository". If you unzip your .mdzip project file you'll find <ownedComment> elements like this in XMI: 

<uml:Model xmi:id='eee_1045467100313_135436_1' name='eSchool' visibility='public'>
<xmi:Extension extender='MagicDraw UML 15.1 EAP beta' extenderID='MagicDraw UML 15.1 EAP beta'>
<moduleExtension ignoredInModule='true'/>
</xmi:Extension>
<ownedComment xmi:type='uml:Comment' xmi:id='_15_1EAPbeta_41b01a5_1206031981598_738250_98' body='Author:drck.&#10;Created:21/03/08 03:53.&#10;Title:.&#10;Comment:.&#10;'>
<annotatedElement xmi:idref='eee_1045467100313_135436_1'/>
</ownedComment>
<ownedComment xmi:type='uml:Comment' xmi:id='_15_1EAPbeta_41b01a5_1206032150212_504528_254' body='What is the difference between a Comment and a Note ?'>
<annotatedElement xmi:idref='_15_1EAPbeta_41b01a5_1206032190538_630673_263'/>
<annotatedElement xmi:idref='_15_1EAPbeta_41b01a5_1206032218065_913844_302'/>
<annotatedElement xmi:idref='_15_1EAPbeta_41b01a5_1206033844150_249704_509'/>
</ownedComment>
<ownedComment xmi:type='uml:Comment' xmi:id='_15_1EAPbeta_41b01a5_1206032209466_431076_292' body='A comment can be owned by any element.'>
<annotatedElement xmi:idref='_15_1EAPbeta_41b01a5_1206032534469_292077_402'/>
</ownedComment>
<ownedComment xmi:type='uml:Comment' xmi:id='_15_1EAPbeta_41b01a5_1206032218065_913844_302' body='A Comment may carry a stereotype, like this «answer» Comment does.'>
<annotatedElement xmi:idref='_15_1EAPbeta_41b01a5_1206032315808_587036_340'/>
<annotatedElement xmi:idref='_15_1EAPbeta_41b01a5_1206033294238_506951_465'/>
</ownedComment>

In MagicDraw UML a «documentation» Comment is a special case. Although an <ownedComment> does appear in the XMI project file, the corresponding Comment can't be found in the containment browser; rather, only the owning element is shown in the browser (along with an other owned elements): 

 <packagedElement xmi:type='uml:Class'
xmi:id='_15_1EAPbeta_41b01a5_1206032198918_773500_271'
name='DocumentMe' visibility='public'>
<xmi:Extension extender='MagicDraw UML 15.1 EAP beta' extenderID='MagicDraw UML 15.1 EAP beta'>
<modelExtension/>
</xmi:Extension>
<ownedComment xmi:type='uml:Comment'
xmi:id='_15_1EAPbeta_41b01a5_1206033403960_761781_475'
body='&lt;html&gt;&#10;  &lt;head&gt;&#10;   
&#10;  &lt;/head&gt;&#10; 
&lt;body&gt;&#10;    &lt;p&gt;&#10;      In
MagicDraw UML a
&amp;#160;&amp;#171;documentation&amp;#187;&amp;#160;
Comment is used to display the &#10;      documentation of an
element. Use &amp;#160;&lt;b&gt;Retrieve
Documentation&lt;/b&gt;&amp;#160; &#10;      from a
Comment attached to an Element by a handle.&#10;   
&lt;/p&gt;&#10; 
&lt;/body&gt;&#10;&lt;/html&gt;&#10;'>
<annotatedElement xmi:idref='_15_1EAPbeta_41b01a5_1206032198918_773500_271'/>
<annotatedElement xmi:idref='_15_1EAPbeta_41b01a5_1206033859779_864981_519'/>
</ownedComment>
<ownedRule xmi:type='uml:Constraint'
xmi:id='_15_1EAPbeta_41b01a5_1206035096633_538298_730'
name='constraint' visibility='public'>
<constrainedElement xmi:idref='_15_1EAPbeta_41b01a5_1206032198918_773500_271'/>
<specification xmi:type='uml:OpaqueExpression'
xmi:id='_15_1EAPbeta_41b01a5_1206035096634_102223_731'
visibility='public' body='this=that' language='OCL2.0'/>
</ownedRule>
<generalization xmi:type='uml:Generalization'
xmi:id='_15_1EAPbeta_41b01a5_1206034781959_486860_633'
general='_15_1EAPbeta_41b01a5_1206034776815_532127_610'/>
</packagedElement>


A note is not a true UML model element. In MagicDraw UML the body of a note is not stored in the model "repository". If you unzip your .mdzip project file you'll find that the note's <text> is in fact stored as a custom XMI extension: 

<mdElement elementClass='Note' xmi:id='_15_1EAPbeta_41b01a5_1206034680723_700552_597'>
<elementID xmi:idref='_15_1EAPbeta_41b01a5_1206032198918_773500_271'/>
<properties>
<mdElement elementClass='ColorProperty'>
<propertyID>PEN_COLOR</propertyID>
<propertyDescriptionID>PEN_COLOR_DESCRIPTION</propertyDescriptionID>
<value xmi:value='-6711040'/>
</mdElement>
<mdElement elementClass='BooleanProperty'>
<propertyID>AUTOSIZE</propertyID>
<propertyDescriptionID>AUTOSIZE_DESCRIPTION</propertyDescriptionID>
<value xmi:value='true'/>
</mdElement>
</properties>
<geometry>560, 553, 141, 102</geometry>
<text>This note calls out Element Properties selected in the Element Properties compartment</text>
<elementProperties xmi:value='QPROP:Element:isAbstract^QPROP:Element:name'/>
<active xmi:idref='_15_1EAPbeta_41b01a5_1206034686712_886949_608'/>
</mdElement>