I don't think there's a journal standard for this. An easy and commonly used method is to plot latitude $\delta$ versus longitude $\alpha$, where the aspect ratio is scaled by $\mbox{cos}(\delta_0)$ so the projection is orthonormal at the image center $(\alpha_0, \delta_0)$. Depending on your region size and on $|\delta_0|$, this may or may not come out looking distorted. You might be able to pick a coordinate system (i.e. equatorial or galactic) where the latitude is never large enough to give major distortion.
Another common thing to do, arguably better when you're imaging extended objects, is to use a tangent-plane projection, also called a gnomonic projection. This projection depends on the chosen center, which is usually the image center. It is included in some plotting and analysis packages, but none that I use regularly. I recently coded this up for the Astropy package but haven't really tested it yet.
Projections like Aitoff, Hammer, and Mollweide have been included in many plotting packages, but usually only for whole-sky projections. You could try to write your own versions but I'm not sure it would be worth the trouble.
(Whatever you do, make sure longitude increases to the left since you're looking at the sky not the ground...)