(I'm a new user so I don't have anything to contribute as far as norms here go, but I'm really interested in how to effectively convey information in an accessible way!)
Like others have said, the most obvious downside is colorblind people and people using screen readers. Colorblind people will miss information and so you should make sure the color doesn't convey anything essential, like it does in the Fourier Transform jaska posted.
Adding color may make it harder for people with screen readers to parse the rest of the equation as well. I know some people with screen readers read the TeX source, and using a lot of color will make a complete mess of something that would otherwise be comprehensible. I don't know how the screenreaders that have math support render color, but if it's including it, it will probably make it harder to understand.
To some extent, you'd run into the same screenreader issue with bold and italics. From a google it looks like the ones that have math support do read it, but it would be a less frequent intrusion than some uses of color. If the TeX source is being read, I imagine \mathbf would be less disruptive than \color{#c00}.
But using color can really help people with learning disabilities or who are just daunted by big equations. You can do things with it that you just can't do with bolding, italics, or underlining, and I think it's often much easier to make sense of in an equation.
The other potential downside is that color controls your reader's attention, and you'll send them towards wrong things if you don't use it in a thoughtful way.
After looking at some of Bill Dubuque's posts, I wanted to point out some examples of things I consider really effective uses of color. Like this:
This is a special case of telescopy. For as below we can write the RHS as a product of its term ratios
$$\rm\ g(n)\ =\ \frac{g(n)}{\color{#c00}{g(n-1)}}\ \frac{\color{#c00}{g(n-1)}}{\color{#0a0}{g(n-2)}}\ \frac{\color{#0a0}{g(n-2)}}{\cdots }\ \cdots\ \frac{\cdots}{\color{brown}{g(3)}}\ \frac{\color{brown}{g(3)}}{\color{blue}{g(2)}}\ \frac{\color{blue}{g(2)}}{1}$$
Or this:
[Q: Is there an elementary proof that $\sum \limits_{k=1}^n \frac1k$ is never an integer?]
Hint $\ $ Since there is a unique denominator $\rm\:\color{#C00} {2^K}\:$ having maximal power of $2,\,$ upon multiplying all terms through by $\rm\:2^{K-1}$ one deduces the contradiction that $\rm\ 1/2\, =\, c/d \;$ with $\rm\: d \:$ odd, $ $ e.g.
$$\begin{eqnarray} & &\rm\ \ \ \ \color{green}{m} &=&\ \ 1 &+& \frac{1}{2} &+& \frac{1}{3} &+&\, \color{#C00}{\frac{1}{4}} &+& \frac{1}{5} &+& \frac{1}{6} &+& \frac{1}{7} \\
&\Rightarrow\ &\rm\ \ \color{green}{2m} &=&\ \ 2 &+&\ 1 &+& \frac{2}{3} &+&\, \color{#C00}{\frac{1}{2}} &+& \frac{2}{5} &+& \frac{1}{3} &+& \frac{2}{7}^\phantom{M^M}\\
&\Rightarrow\ & -\color{#C00}{\frac{1}{2}}\ \ &=&\ \ 2 &+&\ 1 &+& \frac{2}{3} &-&\rm \color{green}{2m} &+& \frac{2}{5} &+& \frac{1}{3} &+& \frac{2}{7}^\phantom{M^M}
\end{eqnarray}$$
The prior sum has all odd denominators so reduces to a fraction with odd denominator $\rm\,d\, |\, 3\cdot 5\cdot 7$.
The color completely commands your attention. When I look at the equation in the first example, I don't read it left to right. The first thing I see is the pattern, and then I read out from there. In the second example, I'm trying to match the colors up before I've really read the text.
It works in Bill's posts because understanding how the colored things are connected is central to understanding the post—the color directs your attention right where it needs to go, and you quickly see what he's trying to show you. But if it didn't draw you to the right place, or if wasn't clear what it was supposed to show, you'd be distracted and confused before you even fully read the text. If you're not positive that color will lead your reader in the right direction, it's probably best to avoid it.
Another use might be to highlight a part of a proof or derivation which deserves special attention, or has some things to note about, later in the post.
I think the latter would be a mistake. The reader should understand why there's color as they're reading the proof. It's too prominent to expect a reader to just keep going until you see fit to explain.