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I would recommend either Qrule or SIMMAP. The suitability of a given model is dependent on what type of neutral landscape structure you wish to simulate (e.g., edge fractal dimension, mean patch size, juxtaposition, etc...).
I am not sure what tools you are looking for (not sure what do you want to simulate) but there are few programs that deal with landscape indices:
Fragstats - http://www.umass.edu/landeco/research/fragstats/fragstats.html
Patch Analyst - ArcGIS add-on (link to presentation - http://www.cnr.uidaho.edu/rsgis/docs/Fragmentaiton.pdf)
GRASS GIS have a module for this- r.le or r.li.
SAGA GIS may have some tools, depending what indices you want to calculate (http://www.saga-gis.org/en/index.html).
LandFrag - is something you may have a look at as well (http://placeways.com/products/landfragtool.php)
Placeways does have also software that allows for more extensive calculation, so have look at theirs site.