>Should I use the Trisquel net-installer iso?
Yes. I think that the CD images for installing a graphical environment also
contain the netinstaller, but it doesn't uses the packages already in the CD,
it downloads them from a mirror. I am not completely sure.
>I am assuming there is an option for disabling installation of the desktop
environment.
Yes, there is.
>Also, what web-server should I use?
Web server software is usually very flexible. There is no single server
software that you “should” use. I have used Nginx which is efficient in
resource usage and easy to configure using a text configuration file.
LigHTTPd is also efficient in resource usage, but I do not have experience
with it. Apparently Apache is harder to configure and much less efficient
than the other 2 mentioned server software packages.