I like the question. Though I (a user of Audacity) might be not competent to answer it, I'll tried my best.
(I do not know what VPAT is.)
I looked on 508 shortly and I think there is nothing special that would prevent Audacity comply to it.
Audacity is close to a big step in the development cycle, that is the release of next major stable version.
Support and feedback from users (including the disabled ones) can improve it to suit to their needs.
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{Edit}
I think you will not be interested much in mine chat and will want to skip to
this post below
or to Leland's
post
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Do you just want to know if the program complies to some standards or do you need to see a certificate?
I understand it is rather the second option.
I think that certification is ususally expensive and I would be pessimistic and did not expect it from a free software unless there is a special sponzorschip or support devoted mainly to certification.
I did not read explicite statement that the developpers pay attention to accessibility standards (especcially of different countries). However, from a short listening to developper's list I know they pay attention to keyboard input problems
and that they do tests regarding the reader and its usability with Audacity.
They had feedback from at least one blind user recently right on this forum during short period I am watching it.
I am not layer, I am a user of Audacity. Mainly for fun, and to encourage the devellopers I reviewed 508 shortly.
It is not long at all.
My feeling is that Audacity complies to this norm.
Ofcourse at each stage of develepoment there are known minor issues that are
not related to dissabilites (on keyboard input, fokus, ...) and we can expect there will be a few related to disabilites of this kind. Audacity is very nice program, well structured, and designed so that I see nothing that would be a problem in 508.
As of the minor issues that appear in each development state, three factors are of great impact: Feedback from dissabled people can help to discover problems and/or rise their priorities and their participation in 'alpha' and beta testing
of pre-release builds (if it suits current development course) can avoid its appearance in released verions.
Note that soon, release of Audacity 1.4. stable is planned, which is a major step in development.
Audacity welcomes volunteers. For more how about to join, see Audacity web pages or ask on this Forum.
{{link missing}}
http://audacityteam.org/forum/
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I started with your link, through 508 Law
on
Software applications and operating systems (1194.21)
(I think that section "Video or Multimedia Products (1194.24)" does not apply since 1. "Multimedia products involve more than one media" and 2. a program is simply never similar to video, presentation or like.)
BTW, the preamble is important too, and I do not understand it much. First "Section 508 requires that when Federal agencies develop ..." means that Audacity team is not bounded Section 508 since audacity develepment team is not Federal agency (??). OK, perhaps schools are bound 508 but their servis consists of many components that complement each other which is an adventage.
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I mark bold things I do not know if I should attract the attention to them.
Shortly, 508 requires that the following is possible
a. keyboard only execution
b. non disruppting accessibility features of OS and other producs
c. A well-defined on-screen indication of the current focus.
The focus shall be programmatically exposed so that assistive technology can track focus and focus changes.
(I think this is ok because it infact goes under the test with reader?)
d. Sufficient information about a user interface element ... (is that about images only ?)
Do we have recording level info for blind persons?
e. When bitmap images ...
f. Textual information shall be provided through operating system functions for displaying text. ...
g. ...
h. When animation is displayed, the information shall be displayable in at least one non-animated presentation mode at the option of the user.
i. Color coding shall not be used as the only means of conveying information ...
j. When a product permits a user to adjust color and contrast settings, a variety of color selections capable of producing a range of contrast levels shall be provided.
k. Software shall not use flashing or blinking text, objects, or other elements having a flash or blink frequency greater than 2 Hz and lower than 55 Hz. 
(OK, as of metters the following gives us an escape: 1194.3 General exceptions e) This part shall not be construed to require a fundamental alteration in the nature of a product or its components)
l. ...
The documentation
if on web might go under 1194.22 Web-based intranet and internet information and applications.
otherwise:
1194.41 Information, documentation, and support.
(a) Product support documentation provided to end-users shall be made available in alternate formats upon request, at no additional charge.
(b) End-users shall have access to a description of the accessibility and compatibility features of products in alternate formats or alternate methods upon request, at no additional charge.
(c) Support services for products shall accommodate the communication needs of end-users with disabilities.
This should not be problem, too.