You can reference Mathematica, SystemModeler, and other Wolfram products in your published work just as you would reference a book or any other publication. The standard citation elements are:

Mathematica 10.0

Author: Wolfram Research, Inc.
Title: Mathematica
Edition: Version 10.0
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 2014

A sample citation of this form would be:

Wolfram Research, Inc., Mathematica, Version 10.0, Champaign, IL (2014).

SystemModeler 4.0

Author: Wolfram Research, Inc.
Title: SystemModeler
Edition: Version 4.0
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 2014

A sample citation of this form would be:

Wolfram Research, Inc., SystemModeler, Version 4.0, Champaign, IL (2014).

Mathematica 8.0

Author: Wolfram Research, Inc.
Title: Mathematica
Edition: Version 8.0
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 2010

A sample citation of this form would be:

Wolfram Research, Inc., Mathematica, Version 8.0, Champaign, IL (2010).

Mathematica 9.0

Author: Wolfram Research, Inc.
Title: Mathematica
Edition: Version 9.0
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 2012

A sample citation of this form would be:

Wolfram Research, Inc., Mathematica, Version 9.0, Champaign, IL (2012).

SystemModeler 3.0

Author: Wolfram Research, Inc.
Title: SystemModeler
Edition: Version 3.0
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 2012

A sample citation of this form would be:

Wolfram Research, Inc., SystemModeler, Version 3.0, Champaign, IL (2012).

Mathematica 8.0

Author: Wolfram Research, Inc.
Title: Mathematica
Edition: Version 8.0
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 2010

A sample citation of this form would be:

Wolfram Research, Inc., Mathematica, Version 8.0, Champaign, IL (2010).

Mathematica 7.0

Author: Wolfram Research, Inc.
Title: Mathematica
Edition: Version 7.0
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 2008

A sample citation of this form would be:

Wolfram Research, Inc., Mathematica, Version 7.0, Champaign, IL (2008).

Mathematica 6.0

Author: Wolfram Research, Inc.
Title: Mathematica
Edition: Version 6.0
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 2007

A sample citation of this form would be:

Wolfram Research, Inc., Mathematica, Version 6.0, Champaign, IL (2007).

Mathematica 5.2

Author: Wolfram Research, Inc.
Title: Mathematica
Edition: Version 5.2
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 2005

A sample citation of this form would be:

Wolfram Research, Inc., Mathematica, Version 5.2, Champaign, IL (2005).

Mathematica 5.1

Author: Wolfram Research, Inc.
Title: Mathematica
Edition: Version 5.1
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 2004

A sample citation of this form would be:

Wolfram Research, Inc., Mathematica, Version 5.1, Champaign, IL (2004).

Mathematica 5.0

Author: Wolfram Research, Inc.
Title: Mathematica
Edition: Version 5.0
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 2003

A sample citation of this form would be:

Wolfram Research, Inc., Mathematica, Version 5.0, Champaign, IL (2003).

If you are citing The Mathematica Book for 5.0, 5.1 or 5.2, you would use:

Wolfram, Stephen: The Mathematica Book, Fifth Edition. Wolfram Media/Cambridge University Press, 2003.

Mathematica 4.2

Author: Wolfram Research, Inc.
Title: Mathematica
Edition: Version 4.2
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 2002

A sample citation of this form would be:

Wolfram Research, Inc., Mathematica, Version 4.2, Champaign, IL (2002).

Mathematica 4.1

Author: Wolfram Research, Inc.
Title: Mathematica
Edition: Version 4.1
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 2001

A sample citation of this form would be:

Wolfram Research, Inc., Mathematica, Version 4.1, Champaign, IL (2001).

Mathematica 4.0

Author: Wolfram Research, Inc.
Title: Mathematica
Edition: Version 4.0
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 1999

A sample citation of this form would be:

Wolfram Research, Inc., Mathematica, Version 4.0, Champaign, IL (1999).

If you are citing The Mathematica Book for 4.0, 4.1, or 4.2, you would use:

Wolfram, Stephen: The Mathematica Book, Fourth Edition. Wolfram Media/Cambridge University Press, 1999.

Mathematica 3.0

Author: Wolfram Research, Inc.
Title: Mathematica
Edition: Version 3.0
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 1996

A sample citation of this form would be:

Wolfram Research, Inc., Mathematica, Version 3.0, Champaign, IL (1996).

If you are citing The Mathematica Book, you would use:

Wolfram, Stephen: The Mathematica Book, Third Edition. Wolfram Media/Cambridge University Press, 1996.

Mathematica 2.2

Author: Wolfram Research, Inc.
Title: Mathematica
Edition: Version 2.2
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 1993

A sample citation of this form would be:

Wolfram Research, Inc., Mathematica, Version 2.2, Champaign, IL (1993).

If you are citing The Mathematica Book, you would use:

Wolfram, Stephen: Mathematica: A System for Doing Mathematics by Computer, Second Edition. Redwood City: Addison-Wesley, 1991.