SharePoint supports displaying other Web pages (presented in an iframe) using the "Page Viewer". The URL for its content could be any web page, including a FlexViewer.
We are in the process of upgrading to sharepoint 2010 and have heard that Microsoft Silverlight 5.0 is the last version they are going to release. Will the equivalent ArcGIS for sharepoint be developed for flex? Adding a page viewer adds a flex application but there is no way to link lists to features on the map.
Plugins are being fade out slowly and this includes both Flex and Silverlight. They are on the same boat. I doubt Esri will invest money on that choice but that is something only Esri can answer. Silverlight is the best integrated Esri GIS software to use with Microsoft Sharepoint. Silverlight is a supported producted till 2021. http://support.microsoft.com/gp/lifean45
That said, for the next 1-2 years Flex and Silverlight are still the best choices for building complex GIS apps, more focused on the enterprise, the user experience, productivity and cost vs development effort. I am assuming that cross-browser and cross-platform compatibilities aren't a concern since you are talking about plugins.
If your goal is to have a single app that is cross-browser and cross-platform and that does not require the power of a RIA or a native app then probably HTML/JavaScript is a good choice. ArcGIS Online templates are a good starting point and wiring some code to bridge the gap between Sharepoint and JavaScript are definetely worthwhile.
Though, if that isn't the case and since you are working with Sharepoint I strongly recommend you to work with Silverlight. It is fully supported on Windows 8 Desktop Mode. You can also migrate it to Metro XAML/C# more easily.
