When you run ./configure, you are telling the configure script to use the defaults for all values.
If you run "./configure --help" (without the quotes, of course), you will see a lot of options to fine-tune your aMule compilation. This is true for most applications you compile, not just aMule.
The important ones for you right now are:
--disable-monolithic disable building of the monolithic aMule app
--enable-amule-daemon compile aMule daemon version
--enable-amulecmd compile aMule command line client
--enable-webserver compile aMule WebServer
--enable-amule-gui compile aMule remote GUI (EXPERIMENTAL)
--enable-cas compile C aMule Statistics
--enable-wxcas compile aMule GUI Statistics
--disable-ed2k don't compile aMule ed2k links handler
--enable-alc compile aMuleLinkCreator GUI version
--enable-alcc compile aMuleLinkCreator for console
--enable-xas install xas XChat2 plugin
--enable-fileview compile aMule file viewer for console (EXPERIMENTAL)
--enable-plasmamule compile aMule plasma applet and engine
Now, those are the defaults. For example, aMule monolithic (full aMule) is enabled by default. You want to disable anything that needs a GUI, and only leave what you want. In your case,
./configure --disable-monolithic --enable-amule-daemon --enable-webserver
should disable the only GUI thing enabled by default (aMule) and enable amuled and amuleweb. You can add "--enable-amulecmd" if you want to that line. Everything else is disabled by default except ed2k, which is a small app used for link handling and it doesn't matter much if you compile it or not in your server.