Jonathan Peelle

Links

The usual suspects: SPM, FSL, FreeSurfer, AFNI, and SUMA.
BrainVISA/Anatomist.
SnPM for nonparametric statistics and SPMd for exploratory data analysis.
MarsBaR region of interest toolbox for SPM
Chris Rorden's excellent MRIcron for visualization
The SPM Anatomy toolbox provides cytoarchitectonic probabilities in MNI space.
The non-stationarity toolbox accounts for non-stationarity in data (e.g. in VBM studies, see Ashburner & Friston, 2000) and permits the use of cluster extent correction for these data within SPM.

Devlin JT, Poldrack RA (2007) In praise of tedius anatomy. NeuroImage 37, 1033–1041. #
Henson RNA, Penny W. ANOVAs in SPM. Technical report. PDF
Kriegeskorte N, Simmons WK, Bellgowan PSF, Baker CI (2009) Circular analysis in systems neuroscience: The dangers of double dipping. Nature Neuroscience 12, 535–540. #
Liu TT (2004) Efficiency, power, and entropy in event-related fMRI with multiple trial types Part II: Design of experiments. NeuroImage 21, 401–413. #
Poldrack RA, Fletcher PC, Henson RN, Worsley KJ, Brett M, Nichols TE (2008) Guidelines for reporting an fMRI study. NeuroImage 40, 409–414. #
Ridgway GR, Henley SMD, Rohrer JD, Scahill RI, Warren JD, Fox NC (2008) Ten simple rules for reporting voxel-based morphometry studies. NeuroImage 40, 1429–1435. #

The SPM annotated bibliography is also a great collection of relevant imaging papers.

Geoff Aguirre has an excellent series of lectures on the fundamentals of fMRI.
Most of the major analysis software packages have mailing lists going back several years with a lot of helpful discussion. I have made particular use of the SPM and FSL archives.
The MRC Cognition and Brain Sciences unit imaging wiki.
Ged Ridgway has some very helpful VBM scripts.
Chris Rorden has an introductory tutorial in neuroanatomy.

An in-progress list of UNIX commands aimed particularly at people with no prior experience.