Choosing and Using Latex 

Personally i feel that latex is a bit bloated and too confusing for first time users. If more effort can be put into front end. It will definitely be the choice of writing. http://openwetware.org/wiki/Word_vs._LaTeX

For LaTEX, I recommend the use of texmaker http://www.xm1math.net/texmaker/ . It just makes everything look more manageable just like word.

Adding URLs in Bibtex with Latex

There has been quite some discussions about how to add urls/websites in your bib file. some use natbib which supports @online or @webpage.

If you prefer not using natbib the other options, you can do this:

@misc{jones07anatomy,
    Author = {M. Tim Jones},
    Title = {IBM Anatomy of the Linux file system},
    Howpublished = {url{http://www.ibm.com/developerworks/linux/library/l-linux-filesystem}},
    Month = {October},
    Year = {2007},
    Note = {Accessed: 12/03/2010}}

Do note that in howpublished which is your url. You may notice I have used url.

For some apparent reason, if you url has strange symbols or is like a protected word for example www.asd.com/DS_129385. PdfLatex throws up an error when it tries to automatically insert $ before these characters and } at the end. If you use url, it encapsulates this and makes everything in order.