Say for example a script begins like this
#!/bin/bash
#$ -S /bin/bash
#$ -l hostname=qn*
and then later down the page the actual script comes into play. My question is what does the "#$" symbol mean or do?
Lines beginning with # are comments. The first line may begin with #!, but it's still a comment to bash and is merely used to indicate the interpreter to use for the file. All other lines beginning with # are absolutely unimportant to bash, whether the next character is $ or anything else.
Are you by any means running on a batch cluster? Like Sun Grid Engine? There might be special meanings in scripts intended to run as a batch job.
https://www.wiki.ed.ac.uk/display/EaStCHEMresearchwik/How+to+write+a+SGE+job+submission+script
Update:
above link blocks when used from stackoverflow.com (works from google.com)
alternatives:
They seem to be parameters for the Oracle (ex-Sun) Grid Engine, look at this SO question or this one.
They are heavily using these kind of comments.