Here few of them....
YASARA Energy Minimization Server: http://www.yasara.org/minimizationserver.htm
Chiron portal: http://troll.med.unc.edu/chiron/login.php
Gromacs energy minimization: http://lorentz.immstr.pasteur.fr/gromacs/minimization_submission.php
ModEval Model Evaluation Server http://modbase.compbio.ucsf.edu/evaluation//
Do you want to perform minimization in order to remove side chain clashes? SCWRL is good for that and quite fast. If you dont want to install any program, you can use CHARMM-GUI for energy minimization online. According to my experience the best way is to use Modeller from the alignments generated from various programs like ClustalW, Muscle, HHPred in case of distant homology. The best scoring servers in the previous CASP9 did actually that and scored their models using PCons, ModFold etc. You may look at the best protein model quality assesment (MQAP) programs in CASP assessment section.