Several industry initiatives exist to maintain transparency and ethical standards among journals and publishers, and these initiatives can help you to determine a journal's reputation.
The Committee on Publication Ethics (COPE) provides advice and guidance on best practices for dealing with ethical issues in journal publishing, aimed primarily at editors and publishers. Journals and publishers can become members of COPE to show that they intend to follow the highest standards of publication ethics. You can search the COPE member list to see if your journal or publisher is a member.
The Directory of Open Access Journals (DOAJ) is an independent index of fully open access (i.e. Gold OA) journals with a mission to increase the visibility, accessibility, and reputation of open access scholarly research journals. Journals must apply for membership and those that meet minimum criteria are added to the directory. Journals that meet all seven criteria additionally receive the DOAJ Seal, which has been awarded to 10% of journals indexed in DOAJ. Journals can be removed from the directory if they cease publishing, are no longer adhering to best practices, have not published enough articles in a calendar year, or for suspected editorial misconduct. You can search the DOAJ to see if your journal or publisher is in the directory.
There are several other industry groups who have similar initiatives to COPE and DOAJ. One that takes a slightly different approach is Retraction Watch, which provides news stories about retracted articles and has a fully searchable database so that you can learn more about the retractions issued by your journals of interest.
The International Committee of Medical Journal Editors (ICMJE) has recommendations for journals to follow but does not check for compliance when journals request to be added to their list of journals.
It should go without saying that the same high standards that are applied to conducting research also apply to writing up and publishing that research; and for many researchers, they know that is the case but nonetheless, some guidance may be helpful to ensure that authors remain compliant with publishing ethics and are aware of the standards that publishers must follow.
Again, a useful resource is the Committee on Publication Ethics (COPE), which provides guidance and education to researchers and authors with the aim of moving "the culture of publishing towards one where ethical practices become a normal part of the culture itself."
Publishing ethics as a topic for research itself has yielded lots of scholarly articles. Among their findings are that unethical research and unethical publishing practices often go hand-in-hand though even if research is carried in ways deemed "normal," unintentionally unethical publishing practices may occur. While medical articles in journals of questionable quality are less impactful than articles in more reputable journals, they are still cited by other works. So clearly the stakes are high, and it is necessary to move towards ethical norms that prevent such work from becoming legitimized by their inclusion in the legitimate work of others. Other unethical practices might be out of the control of the author, such as peer review malpractice: all the more reason to familiarize yourself with accepted norms and expectations in scholarly publishing.