There are basically 2 main options for turning your 5MT into a 6MT.
Option #1:
Transmission Choice: 2007+ LGT Spec B 6MT, 2004, 2005 STI 6MT
Rear Differential Choice: 2007+ LGT Spec B R180, 2004+ STI R180, <2004 Legacy or you can use a regeared stock R160 as well with stock LGT rear axles
Axles: Front - Stock LGT, Rear - 2007+ Spec B or custom Driveshaft Shop Axles
Option #2:
Transmission Choice: 2006+ STI 6MT
Rear Differential Choice: Stock LGT R160
Axles: Front - Stock LGT, Rear - Stock LGT
Etc: DCCD Controller for STI 6MT, 2005+ 2.5i LGT Auto Driveshaft (for Sedan or Wagon based on what you have currently) or 2007+ Spec B Driveshaft, appropriate 6MT flywheel and clutch, 2005 STI front axle seals (recommended), 6MT shift linkage, 6MT shifter, 6MT shift knob (as a note, most donor sets more than likely won't have a knob as most have been robbed from the junkyards ), 6MT slave cylinder, 6MT clutch fork
Quick Pros and Cons to the different components:
<2004 Legacy Differential is not going to be a viscous limited slip (CON)
2007 Spec B 6MT does not contain a limited slip front differential (CON)
2006+ STI 6MT has a 1:1 stepper center differential which allows you to use your Stock R160 on the 07+ cars, if you use an 04-05 STI trans.. the GT 5MT came in 2005-2006 4.11FD 2007-2009 5MT 3.90FD (PRO - Cheaper CON - weaker rear diff if using the R160)
Helpful links for those with lots of time:
Hammer Down's 6MT Swap thread - "the original"
NASIOC's Transmission forums
P/N's:
Spec B Rear Axles - 28421AG03B
R180 Rear Axle Seals – 806732200
05 STi 6MT front half shaft seals:
L/H 806735240
R/H 806735230
Tail Shaft Seal – 806735210