While preparing a poster for SfN, I wondered how I might cite tools that I used like SPM5. I looked at the SPM site and was unable to find a suggested citation. In general how do you cite non-commercial tools that you use in analyzing your data and preparing figures?

Some tools give explicit instructions about the 'proper' way to cite them. For example, FSL (at http://www.fmrib.ox.ac.uk/fsl/index.html indicates one should include a general FSL citation, and provides references for each of the specific tools. Specifically,

Referencing
To quote the relevant references for FSL tools you should look in the individual tool's manual page (or the Analysis Group publications page), and also the FSL overview paper:
S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-219, 2004

And, if you're using BET, you'd include (from http://www.fmrib.ox.ac.uk/fsl/bet2/index...):
If you use BET, please make sure that you quote the following reference in any publications:

S.M. Smith.
Fast robust automated brain extraction.
Human Brain Mapping, 17(3):143-155, November 2002.

If you use the skull and scalp surface extraction functions, please also reference the following:

M. Jenkinson, M. Pechaud, and S. Smith.
BET2: MR-based estimation of brain, skull and scalp surfaces.
In Eleventh Annual Meeting of the Organization for Human Brain Mapping, 2005.


As Mark pints out, however, not all tools are this specific about their preferred citation methods. Perhaps NITRC can help by providing a standardized way for tool and resource developers to indicate their preferences on this, and thus make it more clear when tools have, or have not, established such instructions for their user communities.