You might try overlaying tracks at the UCSC genome browser (is that what you mean?). There's a method where the tracks are semi-transparent. Here are a couple of descriptions/tutorials:

http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html

http://davetang.org/muse/2012/03/15/ucsc-genome-browser-custom-overlap-tracks/

http://biowhat.ucsd.edu/homer/ngs/ucsc.html

http://tools-dev.genereg.net/?p=96

You could also try the GenomeGraphs package from bioconductor:

http://www.bioconductor.org/packages/release/bioc/html/GenomeGraphs.html

That has options for creating plots of data over genomic features - which means you can plot numerous things at once.

There's also those that thing that's done with the modencode data in GBrowse, whereby tracks are overlayed in a 3rd dimension, for instance in figure 1B of this article about Flybase. But I can't find any information on how to make those tracks in GBrowse (it may not be ready for prime time yet).

You might take a look at this Washington University site, an epigenome browser. There's a Nature Methods paper here. You could download the source and work it into a local installation.