Increase List items threshold in SharePoint

We think a lot if want to increase the list view items threshold for the web application because it will be applied to all the site collections that running under the same web application. When we work with list there are many question comes in our mind.

1. SharePoint list supports 3 million item in a list but if threshold limit is crossed the the user will not be able perform many operation including OOTB (Additional filter on list view, grouping, adding new filed or updating existing field). How to avoid such situation?

2. How to increase the threshold for a single list or single web(sub site)?

3. Are there any possibilities for viewing all items/ navigating to all items without any trouble?

4. How majorly system performance impacted if list view threshold increase for the total web application? Are there any best practices?

5. Why Server object model not returning all items from a view when fetching items from specific view?

6. Why OOTB view query is overriding custom CAML query when fetching specific view with CAML query?

and there are more question may arise if you dig further on SharePoint list.

But we can increase the List threshold for a specific list using server object mode / PowerShell scripts.

Server Object Model

using(SPSite site = new SPSite(@"http://kmsnet:5050"))
{
   foreach(SPWeb web in site.AllWebs)
   {
     web.AllowUnsafeUpdates=true;
     SPList lst=web.Lists.TryGetList("MyList");
     if(lst != null)
     {
        lst.EnableThrottling=false;
        lst.Update();       
     }
     web.Update();
     web.AllowUnsafeUpdates=false;
     web.Dispose();
   }
}

PowerShell

Add-PSSnapin Microsoft.SharePoint.PowerShell #-ErrorAction SilentlyContinue

$site = Get-SPSite -Identity "http://kmsnet:5050/"

foreach($web in $site.AllWebs)
{
   $web.AllowUnsafeUpdates = $True;
   $list=$web.Lists.TryGetList("MyList");
   if($list -ne $null)
   {
        $list.EnableThrottling = $False;
        $list.Update();
        Write-Host "List Updated in web" $web.Title
   }
   $web.Update();
   $web.AllowUnsafeUpdates = $False;
   $web.Dispose()
}
$site.Dispose();