SQL server efficiency, comparing date time of latest record and the one under it
Aliasing
The use of T and T1 as aliases in this query made me take twice as long to work out what it is actually doing. I would give these a more meaningful alias.
Brackets
The Where clause contains this:
AND (controllerID in(2,13,28,30,37,40))

The brackets around this are unnecessary and a little confusing. I would only recommend brackets in the Where clause when you are using both AND and OR.
Removing a select
Firstly, let's ask ourselves what this query is doing.
Step 1, get the controllerID's and MAX(dtReading)'s from the ReaderData table.
Step 2, do a datediff of the MAX(dtReading) and the next highest dtReading.
First lets write a simple query to do step 1:
SELECT
    base.controllerID,
    MAX(base.dtReading) AS [Most Recent Reading Date]
FROM ReaderData AS base
WHERE base.CardID = 'FFFFFFF0' 
AND base.controllerID IN (2,13,28,30,37,40)
GROUP BY base_data.controllerID

Now let's bring in the second dtReading:
SELECT
    base.controllerID,
    MAX(base.dtReading) AS [Most Recent Reading Date],
    prior.[Prior Reading Date]
FROM ReaderData AS base
OUTER APPLY
(
    SELECT MAX(extra.dtReading) AS [Prior Reading Date]
    FROM ReaderData AS prior
    WHERE prior.CardID = base.CardID
    AND prior.controllerID = base_data.controllerID
    AND prior.dtReading &lt; base_data.Max_dtReading
) AS prior
WHERE base.CardID = 'FFFFFFF0' 
AND base.controllerID IN (2,13,28,30,37,40)
GROUP BY base_data.controllerID

You'll notice that I changed the CardID = 'FFFFFFF0' and controllerID IN (2,13,28,30,37,40) in the apply to check if it is equal to the value in the main select. It is easier to understand this way, you want to make sure that they are equal, plus it lets you avoid the possible mistake of forgetting to update of the sets of values.
Then we add the datediff:
SELECT
    base.controllerID AS [Controller ID],
    DATEDIFF(SECOND,MAX(base.dtReading),prior.[Prior Reading Date]) AS [Elasped Time]
FROM ReaderData AS base
OUTER APPLY
(
    SELECT MAX(extra.dtReading) AS [Prior Reading Date]
    FROM ReaderData AS prior
    WHERE prior.CardID = base.CardID
    AND prior.controllerID = base_data.controllerID
    AND prior.dtReading &lt; base_data.Max_dtReading
) AS prior
WHERE base.CardID = 'FFFFFFF0' 
AND base.controllerID IN (2,13,28,30,37,40)
GROUP BY base_data.controllerID

Here I took the liberty of aliasing the returned columns to make them a little easier on the eye for the end user, as well as capitalising keywords.
There is no agreed upon standard to SQL, so feel free to re-lowercase everything, but conventionally SQL is written with keywords in ALL CAPS
Performance Increases
The query I walked through above should perform better than the one in the question as it avoids the sub-select.
I would make sure that the ReaderData table is properly indexed, this can and will drastically speed up queries and make sure that the statistics on the table are up to date.