Topology plots
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Espript will produce nice Postscript plots from aligned sequences, highlighting secondary structure: http://espript.ibcp.fr . Roman Laskowski's program PDBSUM seems to fulfill a similar purpose.
Pro-origami: http://munk.csse.unimelb.edu.au/pro-origami/ - and see links on its website!
TOPS: http://balabio.dcs.gla.ac.uk/tops/
CCP4's Topdraw is a drawing tool to help you make your own topology drawing.