I have a web server with which the only method of uploading my files to is scp.
It uses a system called Ensim, which creates virtual unix accounts (or
somethign) so my username which I ssh and scp with ends up being
username#domainname.com
ssh lets me log in fine with this name, and other windows scp clients let me use
it as well. The unix scp openssh client unfortunately does not.

I would attach a (one-liner) patch I have to fix this, but I can't see anywhere
to attach it...
Anyway, it just involves changing the if statement on line 1016 of scp.c to add 
&& c != '#'
to it.