Votre première requête est la plus proche, sauf que vous n'avez pas inclus tous les case en fonction agrégée. Il semble également que vous n'ayez pas besoin de certaines colonnes dans group by clause :
select
[Encounter Number],
Proc1 = max(CASE When [Encounter Proc Sequence] = '1' Then [Procedure Code (Enctr)] END),
SvcDate1 = max(Case When [Encounter Proc Sequence] = '1' Then [Date of Service] END),
Surgeon1 = max(CASE When [Encounter Proc Sequence] = '1' Then [Surgeon] END),
Proc2 = max(CASE When [Encounter Proc Sequence] = '2' Then [Procedure Code (Enctr)] END),
SvcDate2 = max(Case When [Encounter Proc Sequence] = '2' Then [Date of Service] END),
Surgeon2 = max(CASE When [Encounter Proc Sequence] = '2' Then [Surgeon] END),
Proc3 = max(CASE When [Encounter Proc Sequence] = '3' Then [Procedure Code (Enctr)] END),
SvcDate3 = max(Case When [Encounter Proc Sequence] = '3' Then [Date of Service] END),
Surgeon3 = max(CASE When [Encounter Proc Sequence] = '3' Then [Surgeon] END)
--- etc.
from EncounterProc
where [Date of Service] between '20090101' and '20091231'
and [Procedure Code (ENCTR)] is not null
group by [Encounter Number], [Encounter Proc Sequence]
