LaTeX and Physics Publication Advice

Advice:

When editing or adding to a paper, try to keep generally to the same style as the original author
If you reverse a change someone has made, explain to them why the change was less preferable.
To render quotes, use pairs of backticks and single quotes rather than double quotes, e.g. ``Phrase In Quotes''.
Equation formatting:

Roman vs. italic fonts in equations: Variables should be italic, common function names (sin, cos, exp, etc.) should be roman. Also, names, acronyms, initialisms, abbreviations, units, chemical elements, and isotopes (like "He") should be roman. Indices should be italic. For example f_{\mathrm{Steiner}}(x)=\cos x_{\mathrm{SFHo}} gives $$ f_{\mathrm{Steiner}}(x)=\cos x_{\mathrm{SFHo}} \, . $$ To format isotopes, consider ^{208}\mathrm{Pb} which when formatted becomes $ ^{208}\mathrm{Pb} $ .
Always put a space between a numerical quantity and it's associated unit, for example 1.4~\mathrm{M}_{\odot}. I use roman font for a "solar mass" (which is used as a unit here) and put a sticky space (~) to avoid line breaks between the quantity and the unit. This is rendered as $$ 1.4~\mathrm{M}_{\odot} \, . $$ This is a difficult example because I have found that not everyone agrees about whether or not $ \mathrm{M}_{\odot} $ is a unit (roman) or a symbol (italic) in this context. I prefer the former.
If entering a negative number in text mode, you will need to use, e.g. $-$3.14 rather than -3.14 to ensure you get a "minus sign" rather than a "en dash".
In equations, always use resizable parenthesis and brackets if the terms inside are likely to be larger than one standard line. For example \left(\frac{a}{b}\right) rather than (\frac{a}{b}).
If an equation is larger than one standard line, prefer placing it in an equation environment rather than putting it in the text. Avoid using \frac for in-text fractions, and just use / instead.
If you need to nest parentheses in equations, then alternate between parentheses, square brackets, and braces, e.g. $$ \left\{c+\left[b+ \left\{y+\left[1-\cos \left( x^2 \right)\right]^3\right\}^{(a+1/2)} \right]\right\} \, . $$ Avoid nesting parentheses in text.
Equations need to be placed inside the usual structure of a sentence. If they are at the end of a sentence, use \, . to place a period in the equation. If an equation appears in the middle of a sentence, it may need no punctuation at all. Note that using \, in a equation creates a space, in order ensure the reader understands that the punctuation (comma or period) is not part of the equation. In prose, a comma or period should not be preceeded by a space.
For multiline equations, use eqnarray. A basic schema is
```
		  
		  \begin{eqnarray}
		  f(x) & = & \sin \left( x + y^2 \right) \nonumber \\
		  && + \cos \left ( y + x^2 \right) \, ,
		  \end{eqnarray}
		
```
When rendered, this appears similar to $$ \begin{eqnarray} f(x) & = & \sin \left( x + y^2 \right) \nonumber \\ && + \cos \left ( y + x^2 \right) \, , \end{eqnarray} $$ where the plus operator appears to the right of the equals sign to indicate that it refers to an additional term on that side. Note how, in the previous sentence, I use /, , to place the equation inside the sentence and continue the sentence after the equation. You can use \right. and \left. to invisibly close parentheses before starting a new line and \nonumber to ensure that the first line of the equation is not numbered by the document class.

Figures:

All text inside the figure should be no smaller than the main text in the body of the paper. In some cases, where multi-panel figures are used, this means you will need to create a new version of the figure which larger text labels.
Make sure, inasmuch as is possible, that the figure is readable if it is converted to a grayscale image and that dots and dashes are used, if necessary, to distinguish between colors.

Spacing: ensure there is at least one space before references and parenthetical phrase (this is a parenthetical phrase). I often use a tilde (~) or "sticky space" to create a space which will not create a line break. For example, Ref.~\cite{Steiner00qp} ensures a space between "Ref." and "[1]". If the sentence ends before the parenthetical phrase, then put no space between the right parenthesis and the period. If the sentence continues, put a space between the right parenthesis and the next word. If the parenthetical phrase is a sentence on its own, then use the format sentence one. (sentence two.) sentence three.
Citations should occur inside the sentence or phrase where they occur. For example, if they are at the end of a sentence, use end of the sentence~\cite{Steiner00qp}., not end of the sentence.~\cite{Steiner00qp}. Note that sentences should not start with a "cite" command. Start them with "Ref." instead, e.g. Ref.~\cite{Steiner00qp} showed that.... You may sometimes refer to author names, e.g. Steiner et al.~\cite{Steiner00qp} showed that..., but make sure not to use this as a way to name your friends and marginalize your competitors.
Capitalization: Capitalize proper names and the first letter of a sentence. Also, you may use capital letters to define an intialism (or acronym). Don't capitalize anything else.