I'm using this area to store subtitles from Opensubtitles
Also sometimes from subtitlesource
I have only included episodes where no transcripts are available yet or the transcript is corrupt.

Season 3

S3E11 Model Behaviour (click)
S3E16 Family Secret (click)

Note the Model Behaviour transcript link is broken on the hynoweb site.

Season 4

4.21 Brothers in Arms (click)
4.22 In the Dark (click)
4.23 Trojan Horse (click)
4.24 Angel of Death (click)


Season 5 (click)

5.01 Bury Your Dead (click)
5.02 Family (click)
5.03 Ex-file (click)
5.04 Identitiy Crisis (click)
5.05 Leap of Faith (click)
5.06 Chimera (click)
5.07 Requiem (click)
5.08 Designated Target (click)
5.09 Lost and Found (click)
5.10 Corporal Punishment (click)
5.11 Tribes (click)
5.12 Stakeout (click)
5.13 Dog Tags (click)
5.14 Internal Affairs (click)
5.15 In the Zone (click)
5.16 Recoil (click)
5.17 About Face (click)
5.18,5.19 Judgment Day (click)

Season 6

6.01 Last Man Standing (click)
6.02 Agent Afloat (click)
6.03 Capitol Offense (click)
6.04 Heartland (click)
6.05 Nine Lives (click)
6.06 Murder 2.0 (click)
6.07 Collateral Damage (click)
6.08 Cloak (click)
6.09 Dagger (click)
6.10 Road Kill (click
6.12 Caged (click)
6.13 Broken Bird (click)
6.14 Love and War (click)
6.15 Deliverance (click)
6.16 Bounce (click)
6.17 South by South West (click)
6.18 Knockout (click)
6.19 Hide and Seek (click)
6.20 Dead Reckoning (click)
6.21 Toxic (click)
6.22 Legend 1 (click)
6.23 Legend 2 (click)
6.24 Semper Fidelis (click)
6.25 Aliyah (click)


Season 7

7.01 Truth or Consequences (click)
7.02 Reunion (click)
7.03 The Indside man (click)