From a bit of research for myself this week - the best software I've found is called smtm (Show Me The Money).
http://dirk.eddelbuettel.com/code/smtm.html
It provides a fair bit of functionality but is quite simple. It seems to get the stock data from finance.yahoo.com. Charting is very simple - it seems to draw static charts using GNUPlot, so there's not line drawing tools and you can't "hover" the mouse above various points to get the data. However it provides a lot of charting options and various statistical analysis tools. It's probably a good place to start.
Daniel