Since you say you are writing physics articles: the most popular class for physics articles is REVTeX (use latest version by \usepackage{revtex4-1}
, which is now sufficiently bug-free to be recommended over the previous version). It is the class for APS an AIP journal submissions, since it hooks directly into their internal workflow for metadata extraction, draft versions for referees, reference checking, and so on and it allows the distinctive features of those publishers' journals (such as the RMP reference formatting, the PRB superscript citations, combining and collapsing multiple citations into one reference (using proper journal style for 'ibid' etc), two-column-wide equations when necessary, and so on). It also allows accurate length estimations (important for PRL submissions).
It's also possible to use revtex with some tweaks for submissions to other journals (Nat. Phys., NJP and others), but check if the journal you want to submit to has its own preferred documentclass because using it will smooth the process and get your article into print that much more quickly and with fewer mistakes introduced during copyediting. Some of the journal-specific documentclasses do not exist on CTAN and need to be searched for and downloaded from the publishers' web sites.
Generally it's best to keep it simple: avoid fancy TeX tricks such as defining your own macros that do more than just save keystrokes; avoid non-standard packages (things like natbib, amsmath (not with the IOP class), bm are probably OK, but something like cleveref may not be).
This FAQ answer has general advice (not physics-specific) for using latex for article submissions.