Hi All, I was wondering what popular tool people use to offline in-depth analyse the particular characteristics of an audio file? Offline as in not a plug-in frequency analyser etc. More like what I've seen people use screenshots of in order to prove a point regarding "possible clipped samples" and so forth? Thanks!

I use Adobe Audition, which is no longer available. It's predecessor, Cool Edit Pro, can still be found though. A comparable application is Sony Sound Forge.
 
Here's an interesting tool for comparing two or more mixes to one another, either for consistency within an album or to compare your stuff to similar commercial music: http://www.toscanalyzer.org/index.php/en/
 

I use NCH's Wave Pad ( http://www.nch.com.au/wavepad/index.html  ) to view and edit my exported files. It displays the file so I can see the peaks and if I have any clipping, overs, or have too much compression in the project.
Of course, looking at a file doesn't really tell the whole story but it does provide information that you can't get just by listening necessarily.

Audition is still available.  They have just switched to a crappy for of selling it.  It is a cloud based subscription that makes you pay a monthly fee indefinitely.

WAVELAB

It depends on what you're looking for and what your technical level is.
 
I use SoundForge for straightforward stuff.
 
Octave (http://www.gnu.org/software/octave/) can do virtually anything, but let's just say it's a little bit technical.

BTW, I have both, but prefer Sound Forge to Audition.  Never hurts to try the demo of all of the mentioned and see which you feel more comfortable with

Another FYI, current version of Sound Forge and Audition are 32-bit.  The new release of Audition (June 17th) will be 64-bit

SF

Here is a free solution http://waveshop.sourceforge.net/ quick, easy and 64bit (if it matters)