I usually perform mapping of reads to reference genes or genomes using bowtie, that yield an output SAM mapping file. I can import and view such SAM files into CLC Genomics Workbench, but I'm looking for a freeware software allowing a graphical view of mapping files.
I'd give artemis a try: www.sanger.ac.uk/resources/software/artemis/ though I think you'll need to convert your SAMs to BAMs first.
The Broad's IGV is one possibility, as already mentioned. Simple java app and runs well on my Windows 7 x64 box. Another is SeqMonk - http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ also runs well under Windows7 x64 on my work box.
If you want to peruse what's available there are several lists out there too (don't know how up to date they are)
http://en.wikipedia.org/wiki/Genome_browser
and the massive list of software (including visualization tools) from seqanswers.com Wiki: http://seqanswers.com/wiki/Software
I have tried IGV, Tablet and Galaxy. IGV is fine, Tablet cannot show two or more SAM files against the same reference, while I cannot find the function to show mapping in Galaxy.
IGV, IGB and Tablet are very useful and interactive. If you have less RAM and lower-end computer but your files are very huge, then I would prefer SAMtools tview, which is pure command line based visualization. For most of the tools, sorted BAM is preferred.
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