I am quite confident that the figure was brushed up with a graphics program. None of the genome browsers I know have this nice positioning of the track descriptions at the right within the track. The scale on the left also shows just the maximum and no 0, I guess most browsers show some tick marks in between.
If you want a really nice figure, you need to save the output of a genome browser as SVG or PDF (PS) and rework it a little bit e.g. inkscape or adobe illustrator.
The most popular is I guess UCSCs genome browser, but popularity does not equal nice figures.
From UCSC genome browser you can export to PS or PDF (click PDF/PS in the top bar) and then edit with a vector graphics editing program like Illustrator or Inkscape. I would recommend tweaking the browser settings to remove light blue gridlines prior to export.
From IGV you can export a few types of images, including svg, but I personally don't think the figures end up looking as good.
Since this question has been resurrected, I'll add karyoploteR to the list of available tools. It's an R/Bioconductor package to plot data on genomes and can work with BAM files or BigWigs (and many other formats, actually).
Great suggestion. Thanks!