I’ll make the (overdue) part two relatively simple. Please note that it is based on my experiences in 2008. Some things might change. Link to part one is here.
|Reference||LaTeX has the Bibtex addition and with softwares like Jabref, it is really easy to manage||The 2007 Office improves their referencing library. It’s alright for short papers, but it is pale in comparison to Latex|
|Mathematics||Math and equation package||Equation Editor|
|Basic Layout||LaTeX automatically generates basic layout suitable for scientific papers.||There are themes you can use in Word, but usually it would require some tweaking to make it look nice for scientific papers.|
|Advanced Layout||Need to learn a lot about LaTeX before you can do your own advanced layout. There are themes available as well, but it still requires some knowledge if you want to tweak it around.||It’s “What You See Is What You Get” type, so it’s definitely easier. Bringing consistency to the layout would be a bigger problem here.|
|Tables||Complicated to read in the LaTeX code. Needs extra packages to to add colors .||Just click on the generate table button and you can see and customize how you want the table to look like.|
|Spell and grammar checking||Separate installation of spell checking is required, and there’s no grammar checking||Both are available. Grammar checking is good for spotting silly mistakes (especially for a non-native speaker like me 😉 )|
|Cross referencing||Make a label of the section / table / whatever you want to refer, and refer it.||Given that you properly make headings, figure, tables, and such, there is a drop down list where you can just choose.|
I would say that all in all, LaTeX would be much more suited towards writing the thesis, due to consistency (it rarely crashed!) and its ability to handle a long document, forcing you to think about referencing from day one, and structuring.
LaTeX would also be good for scientific paper because usually you can just use the template provided, and if not, the basic LaTeX document looks very scientific already.
For other things, like writing a short essay paper or a novel (what I’m doing right now), I’d choose Microsoft Word any day.