Minion definitely has a Latex math package. I think Utopia, and therefore the spin-off Heuristica has a math set for Latex too.

Have a look the CTAN Free Math Font Survey. I personally use Utopia with the fourier math package, simply calling \usepackage{fourier}. If you want something that looks more professional, without using XeLaTeX or installing otf fonts for LaTeX, you can buy Utopia Expert and call \usepackage[expert]{fourier} (all you need to do is to add the .pfb files where needed, all the rest is already installed). I have not tried that option, I have installed Utopia Standard instead,

Can you post a typical page of your thesis, compiled with the different options that you're considering? Certain features of the content may make one choice better than another. For instance, one of my students is currently writing his thesis and is using Palatino through mathpazo. In certain sections, there are a lot of subscripted is and js, and I find these hard to disinguish since Palatino has very little curl in the j.

It is also true that Palatino is a lighter font, and New Century Schoolbook is heavier. Requirements on margins and point size may also work better with one choice or the other. Because NCS is so dark, I often find pages set to the full width in 12+ pt sizes to be too much.

Best wishes, Stephen

I wrote my thesis before TeX even existed. I often use fourier to reformat papers on the arXiv before reading them on screen. My formats are thus far from those of a thesis. You can have a look at http://www.iro.umontreal.ca/%7Eboyer/griggs/

Added: Above I used \usepackage[upright]{fourier} to get upright capitals and greek letters in equations. After that I called a second package to use the Utopia Std font I had installed.

Concerning indexed indices, I tend to avoid them because there is no appropriate "opticals" for small sizes. Also, the fourier package has very few options. If you don't have the expert fonts, I would say there is no option (the "upright" option being used for French math). Here is the ams testmath.tex file compiled with fourier, no frills added.

http://www.iro.umontreal.ca/~boyer/typophile/testmath.pdf

You will see that \mathcal looks like the \mathscr of the mathrsfs package. If you want the cal font you are used to, you need to declare it yourself (I call it \mathcalus).

If you're willing to put up with the Times (New) Roman look, there is STIX (and XITS). Would not be surprised if both were on CTAN.

The xits fonts were already in the distribution of MacTeX 2010. They should come with MacTeX 2011 too. So does the fourier package. There is no need to fetch.

In the end, I decided to go with Palatino/mathpazo. Thanks at sgh for pointing out that indeed NCS is very heavy. My guidelines require a 12pt font, and after looking at some pages, I decided it is just not acceptable. I still think it might be a good choice for e.g. a thesis in liberal arts.
Small indices are not really an issue. My thesis is more CS than math-related, and there are few pure calculations. Rather lot's of relational and set notation.

In fact this is also why I decided not to go with Utopia and fourier or mathdesign, or with Times and mathpmx or txfonts. I know that several famous journals in my field go with a times-look. But calligraphic math-symbols, such as \mathcal{R} which I make heavy use of, just stand out way too much.

Thanks very much for your feedback everyone, especially pointing me towards the Math Font Survey.

Mathpazo gives very nice results indeeds.

> calligraphic math-symbols, such as \mathcal{R} which I make heavy use of, just stand out way too much.

Those symbols come from separate fonts and can be changed by calling other packages. For instance (with MacTeX 2011 and I presume texlive 2011), there are at least two packages that do just that. You can use \usepackage{eucal} or \usepackage[scaled=0.95]{esstixcal} (with the scale you want). With Fourier, I sometimes just add the two lines (after calling fourier)

\DeclareSymbolFont{cmsy}{OMS}{cmsy}{m}{n}
\DeclareSymbolFontAlphabet{\mathcal}{cmsy}

which give the cal font you get by default with mathpazo. The blackboard and the frak fonts can also be changed with the packages esstixbb and esstixfrak. I like inconsolata as the mono font (\usepackage[scaled=0.95]{inconsolata}).

The mathalfa LaTeX package of Michael Sharpe provides an easy way to change the fraktur, calligraphic, and script math alphabets. The documentation also provides a nice summary of the existing options.

That is a nice and well documented package. Thanks.