Font Setup for an Academic Thesis, no Computer Modern Wanted

mathpazo is a nice alternative, as suggested in a comment. My favorite alternative, however, is the LinuxLibertine family: Libertine for the serif font, Biolinum for the sans-serif, and the font is "complete" in the sense that you will have all the shapes you could wish (slanted, bold, small caps) as well as greek letters. You should definitely have a look at the libertine package.

Edit: Useful comment from Christian Clason: You can combine this with the newtx math fonts:

\usepackage[libertine,cmintegrals,cmbraces,vvarbb]{newtxmath}

and (if necessary) inconsolata for the monospace font

\usepackage[scaled=0.95]{inconsolata}

EDIT: Be aware that on MiKTeX the package inconsolata has a new name and you need to call

\usepackage[scaled=0.95]{zi4}

See also here.

For my PhD-Thesis I used the (in my view awesome) classicthesis, wich uses the Palatino, Euler and Bera Mono typefaces, which seemed like a nice choice.