Wikipedia:Citing sources
It is preferable not to clutter articles with information best left to the references. Interested readers can click on the ref to find out the publishing journal:

N In an article published in The Lancet in 2012, researchers announced the discovery of the new tissue type.[3] 
Y Researchers announced the new tissue type in 2012.[3] 
Simple facts such as this can have inline citations to reliable sources as an aid to the reader, but normally the text itself is best left as a plain statement without in-text attribution:

Y By mass, oxygen is the third most abundant element in the universe after hydrogen and helium.[4]

Dealing with unsourced material: If an article has no references at all, then:

If the entire article is patent nonsense, tag it for speedy deletion using criterion G1.
If the article is a biography of a living person, it can be tagged with {{subst:prod blp}} to propose deletion. If it's a biography of a living person and is an attack page, then it should be tagged for speedy deletion using criterion G10, which will blank the page.
If the article doesn't fit into the above two categories, then consider finding references yourself, or commenting on the article talk page or the talk page of the article creator. You may also tag the article with the {{unreferenced}} template and consider nominating it for deletion.
For individual claims in an article not supported by a reference:

If the article is a biography of a living person, then any contentious material must be removed immediately: see Biographies of living persons. If the material lacking reference is seriously inappropriate, it may need to be hidden from general view, in which case request admin assistance.
If the material added appears to be false or an expression of opinion, remove it and inform the editor who added the unsourced material. The {{uw-unsourced1}} template may be placed on their talk page.
In any other case consider finding references yourself, or commenting on the article talk page or the talk page of the editor who added the unsourced material. You may place a {{citation needed}} or {{dubious}} tag against the added text.

Citation templates and tools: Citation templates can be used to format citations in a consistent way. The use of citation templates is neither encouraged nor discouraged: an article should not be switched between templated and non-templated citations without good reason and consensus – see "Variation in citation methods", above.
If citation templates are used in an article, the parameters should be accurate. It is inappropriate to set parameters to false values to cause the template to render as if it were written in some style other than the style normally produced by the template (e.g., MLA style).

Metadata: Citations may be accompanied by metadata, though it is not mandatory. Most citation templates on Wikipedia use the COinS standard. Metadata such as this allow browser plugins and other automated software to make citation data accessible to the user, for instance by providing links to their library's online copies of the cited works. In articles that format citations manually, metadata may be added manually in a span, according to the COinS specification.

Citation generation tools: Please check the output of these tools for accuracy when the citation is generated.

The visual editor helps users format, insert, and edit sources by simply providing a DOI, URL, ISBN etc., see WP:REFVISUAL.
The citation generation tool of the Visual Editor (WP:REFVISUAL) can also be used when editing the article source, for users who have enabled the 2017 wikitext editor in their preferences.
Citer is an all-purpose tool that generates complete citations
User:Ark25/RefScript, a JavaScript bookmarklet – creates references in one click, works for many newspapers
User:V111P/js/WebRef, a script or bookmarklet automating the filling of the {{cite web}} template. You use the script on the page you want to cite.
User:Badgettrg, Biomedical citation maker. uses Pubmed ID (PMID) or DOI or PMCID or NCT. Adds links to ACP Journal Club and Evidence-Based Medicine comments if present.
WP:ReFill – adds titles to bare url references and other cleanup
Template:Ref info, which can aid evaluating what kind of citation style was used to write the article
Based on Citoid:
Cite templates in Visual Editor
User:Salix alba/Citoid a client for the mw:citoid server which generates Citation Style 1 templates from urls.
Hosted on tools.wmflabs.org:
Wikipedia:refToolbar 2.0, used in the Source Editor
Citation bot
Yadkard: A web-based tool for generating shortened footnotes and citation using Google Books URLs, DOI or ISBN. Also supports some news websites.
Wikipedia template filling – generates Vancouver style citations from PMIDs (PubMed IDs).

Duplicate reference finders: Finding duplicate references by examining reference lists is difficult. There are some tools that can help:

AutoWikiBrowser (AWB) will identify and (usually) correct exact duplicates between <ref>...</ref> tags. See the documentation.
URL Extractor For Web Pages and Text can identify Web citations with the exact same URL but otherwise possibly different. Most differences are not significant, but sometimes different page numbers from the same URL are cited. Occasionally references to the same Web page might be followed by different non-significant tracking parameters (?utm ..., #ixzz...), and will not be listed as duplicates.
Step 1: click "Enter URL", enter (paste) the URL of the Wikipedia article and click "Load",
Step 2: tick "Only Display duplicate URL addresses" (which unticks "Remove duplicate addresses")
Optional: Tick the radio button "Do not show", tick the box at the beginning of its line, and enter (paste) into the box web.archive.org,wikipedia,wikimedia,wikiquote,wikidata,worldcat
Step 3: Click Extract.
Then the duplicates will be listed, and must be manually merged. There will often be false positives; web.archive.org URLs, in particular, are a nuisance as they contain the original URLs, which show as duplicates. The optional part of Step 2 eliminates the archive URLs, but unfortunately the list of duplicates includes the archived pages. The wiki* URLs are less of a problem as they can just be ignored.

Programming tools: Wikicite is a free program that helps editors to create citations for their Wikipedia contributions using citation templates. It is written in Visual Basic .NET, making it suitable only for users with the .NET Framework installed on Windows, or, for other platforms, the Mono alternative framework. Wikicite and its source code is freely available; see the developer's page for further details.
User:Richiez has tools to automatically handle citations for a whole article at a time. Converts occurrences of {{pmid|XXXXXXXX}} (PubMed) or {{isbn|XXXXXXXXXX}} to properly formatted footnote or Harvard-style references. Written in Ruby and requires a working installation with basic libraries.
pubmed2wikipedia.xsl an XSL stylesheet transforming the XML output of PubMed to Wikipedia refs.

Reference management software: Reference management software can output formatted citations in several styles, including BibTeX, RIS, or Wikipedia citation template styles.

Comparison of reference management software – side-by-side comparison of various reference management software
Wikipedia:Citing sources with Zotero – essay on using Zotero to quickly add citations to articles. Zotero (by Roy Rosenzweig Center for History and New Media; license: Affero GPL) is open-source software with local reference database which can be synchronized between several computers over the online database (up to 300 MB without payment).