Intro

Best practices are, and rightfully so, always a much sought-after topic. There are various kinds of best practices:

Microsoft best practices. In real life, these are the most important ones to know, as most companies implementing SharePoint best practices have a tendency to follow as much of these as possibly can. Independent consultants doing architecture and code reviews will certainly take a look at these as well. In general, you can safely say that best practices endorsed by Microsoft have an added bonus and it will be mentioned whenever this is the case.
Best practices. These practices are patterns that have proven themselves over and over again as a way to achieve a high quality of your solutions, and it's completely irrelevant who proposed them. Often MS best practices will also fall in this category. In real life, these practices should be the most important ones to follow.
Practices. These are just approaches that are reused over and over again, but not necessarily the best ones. Wiki's are a great way to discern best practices from practices. It's certainly possible that this page refers to these "Practices of the 3rd kind", but hopefully, the SharePoint community will eventually filter them out. Therefore, everybody is invited and encouraged to actively participate in the various best practices discussions.

This Wiki page contains an overview of SharePoint 2013 Best Practices of all kinds, divided by categories.

Performance

This section discusses best practices regarding performance issues.

http://gallery.technet.microsoft.com/The-SharePoint-Flavored-5b03f323 , the SharePoint Flavored Weblog Reader (SFWR) helps troubleshooting performance problems by analyzing the IIS log files of SharePoint WFEs.
http://gallery.technet.microsoft.com/PressurePoint-Dragon-for-87572ee1 , PressurePoint Dragon for SharePoint 2013 helps executing performance tests.
http://gallery.technet.microsoft.com/Maxer-for-SharePoint-2013-52208636 , a tool for checking capacity planning limits.
http://gallery.technet.microsoft.com/Ping-Dragon-for-SharePoint-70fb299e , a command line tool for pinging SharePoint and getting the response time of a SharePoint page.
http://gallery.technet.microsoft.com/WinPing-Dragon-for-eefb6dd3 , a WPF client for for pinging SharePoint and getting the response time of a SharePoint page.
http://social.technet.microsoft.com/wiki/contents/articles/16218.sharepoint-2013-best-practices-in-depth-performance-counters.aspx , in depth info about performance counters relevant to SharePoint 2013.
http://technet.microsoft.com/en-us/library/ff758658.aspx , TechNet performance monitoring tips
http://www.iis.net/downloads/community/2007/05/wcat-63-(x64) , the Web Capacity Analysis Tool (WCAT) is a lightweight HTTP load generation tool to measure the performance of a web server. Used by MS support in various capacity analysis plans.
Improve SharePoint Speed by fixing a SSL Trust Issue, http://sharepoint-community.net/profiles/blogs/how-to-improve-speed-on-sharepoint-2013
http://technet.microsoft.com/en-us/library/cc262813.aspx , Large Lists
http://technet.microsoft.com/en-us/library/hh395916.aspx , Estimating performance and capacity

2013 Versioning Overview

This section provides an overview of SharePoint 2013 versions.

Beta 1 Preview 15.0.3612.1010
Beta 1 refresh 15.0.3919.1011
Beta 2 interim 15.0.4107.1000
Beta 2 public preview 15.0.4128.1014
Escrow / Release Candidate 15.0.4420.1006
RTM 15.0.4420.1017

Feature Overview

This section discusses best places to get SharePoint feature overviews.

http://www.apps4rent.com/sharepoint-2013-features-comparison.html , nice feature comparison.
http://technet.microsoft.com/en-us/library/jj819267.aspx , extensive SharePoint Online overview.
http://technet.microsoft.com/en-us/library/ff607742(v=office.15).aspx , deprecated features
http://www.andrewconnell.com/blog/archive/2013/01/11/sharepoint-2013-amp-office-365-feature-matrixndashan-easier-way-to.aspx , matrix overview.
http://www.rharbridge.com/www.rharbridge.com/?page_id=966 , nice overview including SharePoint 2013, 2010, 2007, and Office 365.
http://www.fpweb.net/sharepoint-hosting/2013/compare-sharepoint-server-standard-enterprise/ , 2013 standard vs enterprise
http://www.khamis.net/blog/Lists/Posts/Post.aspx?ID=96 , 2013 standard vs enterprise vs foundation

Capacity Planning

http://technet.microsoft.com/en-us/library/jj219628.aspx#HW_Enterprise , info about scaling search.
http://technet.microsoft.com/en-us/library/cc262787.aspx , capacity boundaries

Installation

This section discusses installation best practices.

http://social.technet.microsoft.com/wiki/contents/articles/15289.sharepoint-2013-best-practices-creating-a-development-environment.aspx , provides a detailed explanation how to create a SharePoint 2013 development environment.
http://technet.microsoft.com/en-us/library/cc262749.aspx , system requirements overview
http://technet.microsoft.com/en-us/library/ee662513.aspx , provides an overview of the administrative and service accounts you need for a SharePoint 2013 installation.
http://technet.microsoft.com/en-us/library/cc678863.aspx , describes SharePoint 2013 administrative and service account permissions for SQL Server, the File System, File Shares, and Registry entries.
http://social.technet.microsoft.com/wiki/contents/articles/14500.sharepoint-2013-best-practices-service-accounts.aspx , naming conventions and permission overview for service accounts.
http://www.slideshare.net/michaeltnoel/spcsea-2013-upgrading-to-sharepoint-2013, a methodical approach to upgrading to SharePoint 2013.
http://autospinstaller.codeplex.com/ , Automated SharePoint 2010/2013 installation using PowerShell and XML configuration.
http://autospinstallergui.codeplex.com/ , GUI tool for configuring the AutoSPInstaller configuration XML.
http://social.technet.microsoft.com/wiki/contents/articles/16343.sharepoint-2013-best-practices-setting-up-a-dev-environment-for-windows-apps-and-sharepoint.aspx , describes how to set up a dev environment needed for creating Windows Apps that leverage SharePoint.
http://technet.microsoft.com/en-us/library/jj658588.aspx , installing workflows
Install SharePoint 2013 on a single server with SQL Server
Install SharePoint 2013 on a single server with a built-in database
Install SharePoint 2013 across multiple servers for a three-tier farm
Install and configure a virtual environment for SharePoint 2013
Install or uninstall language packs for SharePoint 2013
Add web or application servers to farms in SharePoint 2013
Add a database server to an existing farm in SharePoint 2013
Remove a server from a farm in SharePoint 2013
Uninstall SharePoint 2013
Install and configure a virtual environment for SharePoint 2013

Upgrade and Migration

This section discusses how to upgrade to SharePoint 2013 from a previous version.

http://social.technet.microsoft.com/wiki/contents/articles/15743.sharepoint-2013-best-practices-upgrading-from-sharepoint-2007.aspx discusses best practices for upgrading from SharePoint 2007 to 2013.
http://social.technet.microsoft.com/wiki/contents/articles/16033.sharepoint-2013-best-practices-migrate-from-sharepoint-foundation-2013-to-sharepoint-server-2013.aspx , upgrade SharePoint Foundation 2013 to SharePoint Server 2013.
http://technet.microsoft.com/en-us/library/cc262483.aspx , SharePoint 2010 to 2013.
http://technet.microsoft.com/en-us/library/cc303436.aspx , upgrade databases from SharePoint 2010 to 2013.
http://www.google.nl/url?sa=t&rct=j&q=download%20proven%20practices%20for%20upgrading%20or%20migrating%20to%20sharepoint%202013&source=web&cd=1&ved=0CEgQFjAA&url=http%3A%2F%2Feu.avepoint.com%2Fassets%2Fpdf%2Fwhite-papers%2Femea%2FSharePoint-2013-Migration-White-Paper.pdf&ei=L2FRUdPHJoqX1AWy44CgBw&usg=AFQjCNHA6Iuoigex0xyHb-EuPdBDIiLrhw&bvm=bv.44158598,d.d2k , PDF document containing extensive info about Proven Practices for Upgrading or Migrating to SharePoint 2013.
http://technet.microsoft.com/en-us/library/ee947141.aspx , upgrade from sharepoint 2007 or wss 3 to sharepoint 2013

Infrastructure

This section discusses infrastructure best practices.

http://technet.microsoft.com/en-us/library/cc263199(v=office.15) , infrastructure diagrams.
http://social.technet.microsoft.com/wiki/contents/articles/16180.sharepoint-2013-best-practices-dealing-with-geographically-dispersed-locations.aspx , dealing with geographically dispersed locations.

Backup and Recovery

This section deals with best practices about the back up and restore of SharePoint environments.

http://technet.microsoft.com/en-us/library/ee663490.aspx , general overview of backup and recovery.
http://technet.microsoft.com/en-us/library/ee428315.aspx , back-up solutions for specific parts of SharePoint.
http://www.slideshare.net/thomasvochten/sharepoint-high-availability-disaster-recovery , good info about disaster recovery
http://technet.microsoft.com/en-us/library/cc748824.aspx , high availability architectures
http://social.technet.microsoft.com/wiki/contents/articles/17195.sharepoint-2013-best-practices-back-up-sharepoint-online.aspx , how to back up SharePoint online?

Database

http://technet.microsoft.com/en-us/library/cc678868.aspx , great resource about SharePoint databases.
http://technet.microsoft.com/en-us/library/ff851878.aspx , removing ugly GUIDs from SharePoint database names.

Implementation and Maintenance

This section deals with best practices about implementing SharePoint.

http://social.technet.microsoft.com/wiki/contents/articles/6575.ten-steps-to-a-successful-sharepoint-implementation-en-us.aspx explains how to implement SharePoint.
http://technet.microsoft.com/en-us/library/ff851878.aspx , rename service applications

Apps

This section deals with best practices regarding SharePoint Apps.

http://technet.microsoft.com/en-us/library/fp161237(v=office.15).aspx , great resource for planning Apps.
http://msdn.microsoft.com/en-us/library/jj163230.aspx, a resource for building apps for SharePoint.

Every day use

http://social.technet.microsoft.com/wiki/contents/articles/16166.sharepoint-2013-best-practices-using-folders.aspx , using folders

Add-ons

This section deals with useful SharePoint add-ons.

http://www.infragistics.com/products/sharepoint/, an collection of web parts for an enterprise dashboard.
http://harmon.ie/Products/Mobile, an app for iPhone/iPad that enhances mobile access to SharePoint documents.

Development

This section covers best practices targeted towards software developers.

http://social.technet.microsoft.com/wiki/contents/articles/13373.sharepoint-2013-what-to-do-farm-solution-vs-sandbox-vs-app.aspx , discusses when to use farm solutions, sandbox solutions, or sharepoint apps.
http://msdn.microsoft.com/en-us/library/office/apps/fp179921(v=office.15) , design patterns for apps.
http://social.technet.microsoft.com/wiki/contents/articles/13637.sharepoint-2013-best-practices-what-client-api-should-you-choose-when-building-apps.aspx , guidelines to help you pick the correct client API to use with your app.
http://msdn.microsoft.com/en-us/library/jj164060(v=office.15).aspx , guidelines to help you pick the correct client API for your SharePoint solution.
http://social.technet.microsoft.com/wiki/contents/articles/16343.sharepoint-2013-best-practices-setting-up-a-dev-environment-for-windows-apps-and-sharepoint.aspx , describes how to set up a dev environment needed for creating Windows Apps that leverage SharePoint.
http://social.technet.microsoft.com/wiki/contents/articles/16353.sharepoint-2013-best-practices-working-with-connection-strings-in-auto-hosted-sharepoint-apps.aspx , discusses how to deal with connection strings in auto-hosted apps

Debugging

This section contains debugging tips for SharePoint.

Use Wireshark to capture traffic on the SharePoint server.
Use a Text Differencing tool to compare if web.config files on WFEs are identical.
Use Fiddler to monitor web traffic using the People Picker. This will provide insight in how to use the people picker for custom development. Please note: the client People Picker web service interface is located in SP.UI.ApplicationPages.ClientPeoplePickerWebServiceInterface.