[Z-man]

Dave,
What you are referring to as "Season 2" is actually only the first half of season 2, aka "Season 2.0."

Thus, the Season 2.0 DVD contains the first half of season two:
Episode 201: Scattered (2005)
Episode 202: Valley of Darkness (2005)
Episode 203: Fragged (2005)
Episode 204: Resistance (2005)
Episode 205: The Farm (2005)
Episode 206: Home, Part 1 (2005)
Episode 207: Home, Part 2 (2005)
Episode 208: Final Cut (2005)
Episode 209: Flight of the Phoenix (2005)
Episode 210: Pegasus (2005)

And the Season 2.5 DVD contains the second half of season two.
Episode 211: Resurrection Ship, Part 1 (2006)
Episode 212: Resurrection Ship, Part 2 (2006)
Episode 213: Epiphanies (2006)
Episode 214: Black Market (2006)
Episode 215: Scar (2006)
Episode 216: Sacrifice (2006)
Episode 217: The Captain's Hand (2006)
Episode 218: Downloaded (2006)
Episode 219: Lay Down Your Burdens, Part 1 (2006)
Episode 220: Lay Down Your Burdens, Part 2 (2006)

Season two was split in half with a 1-2 month gap in the airing of the episodes.

I suspect that the new "Webisodes" will be part of the Season 3 DVD pack.

-Z