I would suggest checking the piano package from Bioconductor. If you use GO categories to define your gene sets you can display them as gene set enrichment networks.

With a bit of custom source code changes I am producing union networks with the same color scale for significance across all conditions/time points.  This works well for presentations (you can make animated GIF for example) or even scrolling through pages/slides. For publication you will have to put images side-by-side. Not as impressive as animation, but still works to convey the point of dynamic process.

In the attached PDF grey nodes are gene sets that were not detected as deregulated (enriched), red - upregulated and blue - downregulated.

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

If you want to visualize the the change of GO enrichments through time you could consider Hive plots (using axes as time points and enrichment values on the axes).

Alternatively you can use D3 to achieve something like this: http://stackoverflow.com/questions/18569581/filtering-data-for-d3-js-sankey-diagrams