Avogadro should be able to submit jobs to both local and remote resources, monitor the progress of the jobs (ideally returning some indication of the progress of the job, such as a plot of the energy) and return the files to the local machine, with minimal intervention from the user.
It should be able to deal with binaries/runscripts for a range of suppported codes, and be able to remember the specific settings for the different applications on each local/remote resource.
Ideally, it should be able to deal with a remote resouces where access if via ssh, but also resources that are running grid software such as Globus, Nordugrid, Unicore etc.
We already have a rudimentary implementation of some of this in the CCP1GUI project (http://sourceforge.net/projects/ccp1gui/)that you are welcome to pillage for anything of use :-)
Marcus has split this idea into a separate project, MoleQueue.