Please see Table 1 titled "Comparative review of reported platforms for simulating control systems for manipulators" of the following paper. References are also given for further details.
Article A systematic review of current and emergent manipulator cont...
In case you are interested in simulating existing industrial robot manipulators: Many vendors of industrial robots also provide good simulators. Usually, these systems work well with their own robots and are limited concerning simulation of custom kinematic chains. Some packages are free, some are not. Examples:
to name a few. There are some other tools by suppliers that do not sell their own robots:
The industrial simulation package tecnomatix (now owned by Siemens) is a very powerful alternative: http://www.plm.automation.siemens.com/en_us/products/tecnomatix/
Then you can also look at "Robotics Simulation Engineer" by Dassault Systemes / DELMIA at http://www.3ds.com/products-services/3dexperience/on-premise/robotics-on-premise/robot-simulation/
Note that the majority of these programs are expensive, but ABB RobotStudio offers a free version and trial use of add-on packages. The simulation of a full dynamic model for a custom manipulator, however, might be very difficult, whereas kinematic simulations of custom kinematic chains can be done after creating them using the "mechanism editor".
Not sure that this helps you properly with your needs - it is admittedly a rather industrially loaded perspective.
SimMechanics would be a good choice given its large physical modeling toolbox with the entire simulink toolbox (communication with MATLAB is very easy and fruitful)
I think the answers proposed are very diverse because the question is not precise enough. When I simulate a new robot during design, software such as CATIA simulates the inverse kinematic model very well. With a virtual mechanism, we can do the inverse kinematic model. If it is an industrial robot, it is better to simulate in a professional environment such as Delmia. Programming under V-Rep does not allow the generation of motion that can be sent directly to the control of a robot. There is also proprietary software such as Kuka Sim from Kuka. You can also use the Adams software to check the dynamics.