Microarray analysis

Image analysis

TIGR spotfinder - http://www.tm4.org
GridGrinder - http://gridgrinder.sourceforge.net/

Normalisation

TIGR again.
Limma - http://bioinf.wehi.edu.au/limma/
VSN - Link

microRNA

miRBase - http://microrna.sanger.ac.uk/
TargetScan - http://genes.mit.edu/targetscan/
miRanda - http://www.microRNA.org

Genome browsers

Ensembl
UCSC
dCode