Try either multi-table update syntax

UPDATE config t1 JOIN config t2
    ON t1.config_name = 'name1' AND t2.config_name = 'name2'
   SET t1.config_value = 'value',
       t2.config_value = 'value2';

Here is a SQLFiddle demo

or conditional update

UPDATE config
   SET config_value = CASE config_name 
                      WHEN 'name1' THEN 'value' 
                      WHEN 'name2' THEN 'value2' 
                      ELSE config_value
                      END
 WHERE config_name IN('name1', 'name2');

Here is a SQLFiddle demo

One way to do this is with a case expression:

UPDATE table_name
SET    name = CASE id WHEN 7  THEN 'Bob'
                      WHEN 34 THEN 'Mike'
              END
WHERE  id IN (7, 34)

Couldn't find a SQL Server 2008 fiddle engine so I had to opt for a SQL Server 2014 ... so not sure if the following will work in SQL Server 2008, but fwiw ...

Setup some sample data:

create table Table1(id int, Date datetime null);
create table Table2(id int, Date datetime);

insert Table1 values (1,null)
insert Table1 values (1,null)
insert Table1 values (2,null)
insert Table1 values (2,null)
insert Table1 values (2,null);

insert Table2 values (1,'2013-01-29 08:50:00.000')
insert Table2 values (1,'2013-01-29 15:28:00.000')
insert Table2 values (2,'2013-01-31 11:56:00.000')
insert Table2 values (2,'2013-03-11 16:08:00.000')
insert Table2 values (2,'2013-01-31 14:04:00.000');

Keeping in mind that we haven't been provided (yet) with any means to determine which rows to match between Table1 and Table2 for a given id value, I'll just let row_number() generate a 'matching' rowid.

And then we'll make use of SQL Server's ability to update Table1 via a derived table definition:

update T1 
set    T1.Date=T2.Date

from   (select row_number() over(partition by id order by Date) as rowid,
               id,
               Date
        from   Table1 
        where  Date is NULL) T1

join   (select row_number() over(partition by id order by Date) as rowid,
               id,
               Date
        from   Table2) T2

on      T1.id    = T2.id
and     T1.rowid = T2.rowid;

And the results:

select * from Table1;

id  Date
--- --------------------
1   2013-01-29T08:50:00Z
1   2013-01-29T15:28:00Z
2   2013-01-31T11:56:00Z
2   2013-01-31T14:04:00Z
2   2013-03-11T16:08:00Z

And here's a SQL Fiddle for the above.

Instead of specifying the same IN list for both Y and A2, specify it only for A2 and make the subquery correlate with T1 on T2.Y = T1.A2, like this:

UPDATE
  dbo.T1
SET
  A1 = (SELECT TOP 1 T2.X FROM dbo.T2 WHERE T2.Y = T1.A2)
WHERE
  A2 IN (ID1, ID2, ...)
;

This way the subquery will pick the topmost row from T2 that matches the key of the T1 row being updated.

Please note also that using TOP n without ORDER BY will result in an arbitrary row being selected. If there can be two or more distinct values of X per Y in T2, it might be a good idea to make the results deterministic by introducing an ORDER BY clause with specific enough set of sorting criteria.

On the other hand, if X stays the same per Y, you are probably storing redundant information in T2. Perhaps, in that case you should move the X column to T1, based on the facts that a) T2.Y appears to be a reference to T1.A2 and b) A2 is the primary key of T1.

You could supply the new values as a table (with the help of the VALUES row constructor), so that you could join it with the target table and use the join in the UPDATE statement, like this:

UPDATE
  tgt
SET
  Column1 = src.Column1,
  Column2 = src.Column2,
  Column3 = src.Column3,
  ...
FROM
  dbo.TargetTable AS tgt
  INNER JOIN
  (
    VALUES
    (1, 'a', 'k', 'x', ...),
    (2, 'b', 'l', 'y', ...),
    (3, 'c', 'm', 'z', ...)
  ) AS src (ID, Column1, Column2, Column3, ...)
    ON tgt.ID = src.ID
;

This for using where clause :

 UPDATE employees SET gender = 'Male' WHERE id IN (1,2,3)

If you want update all rows in table then:

UPDATE employees SET gender = 'Male'  

If you don't care which timestamp is used for which target row, you can match the two tables by joining them on a generated "row number" using e.g. this:

with cn as (
  select id, invoice_id, generated_at, row_number() over (order by id) as rn
  from creditnote
  where status = 'generated'
), pnr as (
  select id, invoice_id, generated_at, row_number() over (order by id) as rn
  from paymentmodeamount
  where payment_mode = 'creditNote'
)
select *
from pnr 
  join cn on cn.rn = pnr.rn and cn.invoice_id = pnr.invoice_id;

This joins the rows based on the ordering of the ID values in the tables creditnote and paymentmodeamount. If you want you can also order the creditnote table by generated_at.

Given your sample data this would return something like this (this is only to demonstrate what the above join does):

id    | invoice_id | generated_at | rn | id    | invoice_id | generated_at        | rn
------+------------+--------------+----+-------+------------+---------------------+---
63725 |        111 |              |  1 | 10101 |        111 | 2018-02-28 14:42:39 |  1
98236 |        111 |              |  2 | 23982 |        111 | 2018-03-30 11:11:11 |  2

Now the above query can be used as part of an UPDATE statement to bring the rows together.

with cn as (
  select id, invoice_id, generated_at, row_number() over (order by id) as rn
  from creditnote
  where status = 'generated'
), pnr as (
  select id, invoice_id, generated_at, row_number() over (order by id) as rn
  from paymentmodeamount
  where payment_mode = 'creditNote'
)
update paymentmodeamount p
   set generated_at = cn.generated_at
from pnr 
  join cn on cn.rn = pnr.rn and cn.invoice_id = pnr.invoice_id
where p.id = pnr.id
  and p.generated_at is null;

This assumes that paymentmodeamount.id is the primary key of the table.

Note that this won't be very fast for large tables.

Online example: https://rextester.com/YXAK25669