Requirements management tools are often similar to IBM Rational DOORS http://www-03.ibm.com/software/products/en/ratidoor
SysML is a modeling language, similar to UML, that some organizations use for Systems Engineering http://sysml.org
Model Based Systems Engineering (MBSE) is the general term for modeling systems (for example with SysML) and then applying computer analysis tools to those models to perform Systems Engineering optimizations.
Google Project Ara made use of MetaMorph Software Tools to help module designers perform PCB layout, component integration, module pricing estimation, package fit check, module performance, and specification compliance. See http://www.metamorphsoftware.com and https://webgme.org
In general, there is a lot of opportunity to modernize MBSE tools and bring them to a wider audience.
There's also a Systems Engineering version of Enterprise Architect (http://sparxsystems.com.au/products/ea/systems.html) that I think is great for the price.
MDAO = Multidisciplinary Design Analysis and Optimization
In practice, the most common systems engineering tools that I've seen are actually excel and powerpoint. Not knocking either of those tools (or the role of systems engineer), but that seems to be the current state of the field.
For much larger projects, or projects of projects (think large engineering systems of systems that take years to design/build/test/deploy), there's all kinds of software available. My company uses Oracle Primavera for this sort of thing.
Also, don't forget Excel. Excel is everywhere and used for all sorts of things it probably shouldn't be used for.
Hope that helps to clarify my prior comment. Happy to discuss more.
I never meant to imply that Microsoft Project is a suitable tool for aiding in any of these things. Anyone crazy enough to try...
But if you want to make a Gantt chart, Project does well enough. The NASA systems engineers I knew certainly used Project for that purpose. Thus I hardly think you can say that it "isn't suitable for systems engineering" as it is useful in creating/viewing/editing one of the key tools of a system engineer's work -- a project schedule.
A key reason Excel is the default is that people have access to it, while Matlab is prohibitively expensive.
One way to break that trend is to choose GNU Octave, the open source alternative to Matlab. The more widely GNU Octave gets used (or similar free tools) the more likely we are to move beyond an Excel by default engineering culture. GNU Octave covers a large percentage of Matlab features and is able to run Matlab code. https://www.gnu.org/software/octave/
There are other tools, like SageMath, that are built on Python and may make an even better Excel alternative for organization that aren't dependent on legacy libraries of Matlab code.
I've been a part of the SymPy team for several years including mentoring GSoC for two of those years.
The problem with SageMath is that you still have to convince people who are familiar with Excel to learn a new environment. Part of the reason why Excel is taught to the undergrads in that civil engineering program is that they use it in their co-op jobs. It becomes a self-perpetuating cycle since they don't learn any alternative as students so they go with what they know in their jobs.