I would try running the subqueries first into a temp table to gather your counts, then pull your total counts. With the way you have the query setup its going to run each of those subqueries once for every line of PCapps, which is why it is taking so long.
Try something like this:
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