SharePoint App Development

List of common SharePoint customizations and how to build SharePoint Apps around them plus how much it is supported by SharePoint 2013

Customization	App Capability	Comments/Limitations/Alternatives
Alternate CSS (in hive)		Apps cannot deploy files to SharePoint's root files/hive. Instead, css can be deployed to SharePoint using a module or app installed event.
Alternate CSS (in module)		Apps can use modules to deploy css to SharePoint, but only to the app web…not the host web. Referencing css from an app web can have inconsistent results in a host web across depending on the users browser and browser settings. As an alternative, a app installed event can be used to deploy css to a host web.
Alternate CSS (apply)		Apps can leverage an app installed event to apply alternate css to a SharePoint site. This is similar to using feature receivers in farm solutions for the same results.
App for Office		Deploying an app for Office inside SharePoint solution is completely new in 2013 and fully supported using apps for SharePoint. This can be a very powerful components to include in solutions, as is outlined in this post
Application Page		Apps cannot deploy files to SharePoint's root files/hive, which includes the layouts folder. As an alternative, web part pages can be deployed through a module or app installed event receiver.
Column		Declarative columns can only be deployed to the app web…not the host web. If you need to deploy columns into the host web (ex: a content syndication hub), you can leverage an app installed event to provision columns programmatically in the host web.
Content Type		Declarative content types can only be deployed to the app web…not the host web. If you need to deploy content types into the host web (ex: a content syndication hub), you can leverage an app installed event to provision content types programmatically in the host web.
Custom Action		Apps support only specific types of custom actions, including ribbon commands and context menus in both the app web and host web. These can be very powerful when combined with dialog boxes, but do not cover the full spectrum of custom actions available to farm solutions (ex: Site Actions menu).
Delegate Control		Apps for SharePoint do not support "Control" elements that can be used with delegate controls in a master page. Delegate controls are a common mechanism for swapping out functionality of a site using a farm solutions (particularly useful with the AdditionalPageHead delegate). As an alternative, the same result can be achieved through the design in a custom master page (ex: place specific html or server controls in the master page).
Feature Receiver		Apps have remote events for "App Installed", "App Uninstalling", and "App Upgraded". All of these can be used in a similar way to feature receivers in farm solutions. It should be noted that app remote events do not implement reliable messaging.
Feature Stapling		Apps can be "stapled" through the app catalog.  This has more flexible rules than traditional stapling, allowing specific sites, managed paths, or site templates to get apps pushed to them. The app catalog even provides a mechanism for app retraction. However, apps installed through app stapling share a single app web (from the app catalog) and app remote events only fire during installation into the catalog. For more information, see my post a few months back on "app stapling".
Field Type		Custom field types require files to be deployed into SharePoint's root files/hive, which is off limits to the app model. As an alternative, apps can easily deploy custom forms that can leverage almost any web/html controls imaginable. Custom field types have been discouraged, so this approach is even better than farm solutions IMO.
Image (in hive)		Apps cannot deploy files to SharePoint's root files/hive. Instead, images can be deployed to SharePoint using a module or app installed event.
List Definition		Apps can deploy custom list definitions, but only to the app web and not the host web.
List Event Receiver		Apps for SharePoint can deploy remote event receivers that provide similar functionality to list event receivers in farm solutions. However, they can only be deployed to lists/libraries in the app web, not the host web.
List Instance		Declarative list instances can only be deployed to the app web and not the host web. If you need a list provisioned in the host web, you can alternatively look at provisioning the list programmatically into the host web using an app installed event.
Master Page (in hive)		Apps cannot deploy files to SharePoint's root files/hive. Instead, master pages can be deployed to SharePoint using a module or app installed event.
Master Page (module)		Apps can use modules to deploy master pages to SharePoint, but only to the app web…not the host web. Referencing a master page from an app web can have inconsistent results in a host web across depending on the users browser and browser settings. As an alternative, a app installed event can be used to deploy a master page to a host web.
Master Page (apply)		Apps can leverage an app installed remote event to apply a master page to a SharePoint site. This is similar to using feature receivers in farm solutions for the same results.
Module		Apps can leverage modules to declaratively deploy files into SharePoint. However, they can only deploy to the app web. As an alternative, a app installed event can be used to deploy files to a host web.
Script (in hive)		Apps cannot deploy files to SharePoint's root files/hive. Instead, script can be deployed to SharePoint using a module or app installed event.
Script (module)		Apps can use modules to deploy script to SharePoint, but only to the app web…not the host web. Referencing script from an app web can have inconsistent results in a host web across depending on the users browser and browser settings. This also poses a cross-domain issue for the script. As an alternative, a app installed event can be used to deploy script to a host web.
Search Configuration		The query side of search is largely re-architected in SharePoint 2013 and supports the export/import of search configuration. Apps for SharePoint can be used to consistently and efficiently deploy a search configuration to a number of sites!
Service Application		Cloud-hosted apps for SharePoint (Provider and Autohosted) can deliver similar functionality to service applications. Apps can have tenancy permissions and configured to make app-only API calls (ex: outside the context of a user). It all depends on the desired integration and capabilities to determine if an app is an acceptable alternative.
Site Definition		Site definitions deploy files into SharePoint's root files/hive, which is not a capability of apps for SharePoint. As an alternative, consider web templates, "app stapling", or controlling the provisioning process.
Theme		Although I would question the sanity of someone looking to create a theme (we seem to change themes in each release of SharePoint), they can be deployed through an app module (to app web) or app installed event (to host web). This includes the new "composed looks" in SharePoint 2013 that include several files (master pages, theme color palette, fonts, images, etc).
Timer Job		An external process (ex: worker role) can deliver similar functionality to a timer job given the app has tenancy permissions and the ability to perform app-only calls. It all depends on the desired integration and capabilities to determine if an app is an acceptable alternative. I did this for media encoding in this solution and for site collection provisioning in this solution.
User Control (controltemplates)		Apps cannot deploy files to SharePoint's root files/hive, which includes the controltemplates folder. As an alternative, user controls can live in the remote web of an app and used in some similar ways to a user control in controltemplates, but not as delegate controls or page directives in SharePoint pages.
Web Service (ISAPI)		ISAPI web services (under the _vti_bin url) are deployed to the root files/hive of SharePoint, which is off limits to apps. As an alternative, "Cloud-hosted" apps for SharePoint (Provider and Autohosted) can host custom web service in their remote web
Web Part		Apps can deploy "App Parts" (also called Client Web Parts) to SharePoint, but these can only have certain types of custom properties (string, int, bool, enum) and cannot use native web part connections. As an alternative, App Parts can leverage postMessage APIs to communicate to SharePoint (and possibly to each other).
Web Part Page		A web part page is simply an .aspx file deployed through a module. Apps support modules, but only to the app web and not the host web. An alternative is to use the app installed event to add the web part page to the host web. I give this a 50% because it would be impossible to add web parts declaratively to the web part page using this approach (would have to be programmatically or through the UI)
Web Template		Web templates live in the solutions catalog of the host web's site collection root. An app installed event can be used to deploy a web template .wsp to the solution catalog, but cannot activate it.
Workflow		Workflow is re-architected in 2013 to be declarative and is completely supported in the new app model.
Workflow Activity		Workflow is re-architected in 2013 to be declarative and is completely supported in the new app model.