Otimize o desempenho das subconsultas

Eu tentaria executar as subconsultas primeiro em uma tabela temporária para reunir suas contagens e, em seguida, extrair suas contagens totais. Com a forma como você configurou a consulta, cada uma dessas subconsultas será executada uma vez para cada linha de PCapps, e é por isso que está demorando tanto.

Tente algo assim:

declare @t table (Computer varchar(10), Sequence int, Site varchar(3), SoftwareName varchar(20), OS varchar(20) )

insert into @t values
 ('C1',1,'BKN','Adobe Acrobat','Win7')
,('C2',1,'BKN','Adobe Acrobat','Win7')
,('C3',1,'BKN','Adobe Acrobat','Win7')
,('C1',1,'BKN','AutoCAD LT ','Win7')
,('C3',1,'BKN','AutoCAD LT ','Win7')
,('B1',2,'CTW','Adobe Acrobat','Win7')
,('B2',2,'CTW','Adobe Acrobat','Win7')
,('B3',3,'CTW','Adobe LT','Win7')
,('B4',3,'CTW','Adobe Acrobat','Win7')
,('A1',2,'CTW','Adobe Acrobat','Win7')
,('A2',2,'CTW','Adobe LT','Win7')
,('A3',2,'CTW','Adobe Acrobat','Win7')
,('X4',3,'CTW','Adobe Acrobat','WinXP')
,('X1',2,'CTW','Adobe Acrobat','WinXP')
,('X2',2,'CTW','Adobe LT','WinXP')
,('X3',2,'CTW','Adobe Acrobat','WinXP')
,('A4',2,'CTW','Adobe Acrobat','Win7');

SELECT 
    Site,
    OS,
    SoftwareName, 
    Sequence,
    COUNT(SoftwareName)  as 'Count'
into #SiteSpecific
FROM @t
group by Site, OS, SoftwareName, Sequence;


WITH PCapps AS (
SELECT DISTINCT
    Computer,
    Sequence,
    Site,
    SoftwareName,
    OS
FROM @t
)
SELECT 
    DISTINCT
    PC.SoftwareName,
    PC.Sequence,
    PC.Site,
    PerSeq.[Count] as 'Win7Installs/seq',
    PerSite.[Count] as TotWin7apps,
    total.[Count] as TotalInstalls 
FROM PCapps pc
inner join (select SoftwareName, Sequence, OS, sum([Count]) [Count] from #SiteSpecific group by SoftwareName, Sequence, OS) PerSeq 
    on PerSeq.SoftwareName = pc.Softwarename 
    AND PerSeq.Sequence = pc.Sequence
    AND PerSeq.OS = pc.OS
inner join (select SoftwareName, Site, OS, sum([Count]) [Count] from #SiteSpecific group by SoftwareName, Site, OS) PerSite 
    on PerSite.SoftwareName = pc.Softwarename 
    AND PerSite.Site = pc.Site
    AND PerSite.OS = pc.OS
inner join (select SoftwareName, sum([Count]) [Count] from #SiteSpecific group by SoftwareName) Total 
    on Total.SoftwareName = pc.Softwarename 
where Pc.OS='Win7'
order by SoftwareName, Sequence, Site