If I were to have people linking back to me, for example to somedomain.com, would it be the same thing if they linked to somedomain.com/?aff=whatever or somedomain.com#aff Do search engines see the ? or # symbols at the end of your link as different link? Meaning, will pagerank be negatively affected by using those symbols?
No, the absolute link is what gets the value, unless your using proper server side redirects, even then the actual value may be less.
# sign in URL is a fragment specifier - a name or id which defines a position within the document. Same URLs with different fragment specifiers counted as the same URL. In opposite, URLs containing different GET parameters (after the ? sign) processed as the different ones. But they can be "glued" due their similarity or redirects.