"Modern" is a somewhat loaded term. You probably want to distinguish between:
- what's functionally modern in the sense of the most technologically cutting edge or elegant ways to get TeX et famille to do your bidding. E.g., via LuaTeX, XeTeX, ConTeXt, LaTeX3, fontspec, microtype, etc.;
- and, contra what's technologically modern, what's stylistically modern (in the sense of leading edge ideas for thesis/book/document design).
You'll get lots of very good info about functional "edge of the envelope" possibilities just by typing some of the keywords mentioned in point 1 above (LuaTeX, etc.) into the searchbox at the top of this page, following links on and off this site, then asking more directed questions here as and when you'd like to learn more. You'll find that the quality of responses increases the sharper the questions you ask.
Another approach might be to search out those users with specialties you're interested in (Joseph Wright for LaTeX3, Aditya for ConTeXt, Harald and Ulrike for seemingly impossible solutions to raw TeX problems, frabjous, Lev Bishop and Andrew Stacey for academic writing, Stefan and Will for, gosh, everything ...) then "follow" the line of the questions they've answered by chasing them individually through their Users pages. This, I think, would be more fruitful than holding out for a consolidated "reference (book, free pdf, website) that would summarize the working of 'modern' latex for scientific works".
As for what's stylistically modern package-wise, you'll probably find ClassicThesis about as close to the edge as likely to be accepted in a science-oriented masters thesis (actually, probably closer to postmodern than modern). Otherwise, check out Tufte-Book for a raft of stylistically interesting ideas.
