Disclaimer: Although writing a chemistry dissertation with open-source software is readily accomplished, it is probably unwise to make a switch from MS Windows after already starting your writing. It is recommended that you make the decision a year-ish early and write at least one hefty report to acclimate :)
OpenOffice.org 3.1 Office Suite:
OOO3 Writer - Word Processor
OOO3 Draw - Drawing Program - I used this to prepare all of my Figures and Schemes saving each one separately with a unique alpha-numeric identifier for easy renumbering at the end.
OOO3 Calc - Spreadsheet - Used to generate tables and graphs
JabRef 4.2 - Java-Based Reference Manager - Fast and flexible, however there is a bit of a learning curve (maybe a few hours) associated with using the "style file," a template that formats your bibliography. I know there are several others out there, but JabRef was easy enough that I could get started with it right away and it is very robust. Documentation on their web site is good, and you will find there the critical plugin for syncing to OOO3.