Currently automake based projects are not very well supported in Eclipse. On the other side ant based projects are really well supported in Eclipse.
To close this gap until one writes a plugin that does it for real I wrote a small build.xml template
for ant that calls configure and make. It allows to generate the auto* files, runs configure with the needed flags and can call the most common targets of Makefiles. It just needs to be placed in the root of an automake based project with the filename build.xml. Eclipse recognizes this as ant build file automatically then and you can easily runnin its targets.
Please test it and give feedback. More ideas and patches are welcome.