They're in production order, except that the two-part episodes have been put together. (If they went strictly by production order or airdate order, they would have two-part episodes split up.)
It's too bad they split the animation of two-parters between different companies. The first part of the Two-Face 2-parter was animated by TMS and is gorgeous. Part Two...eh.
I've heard similar thoughts about "Robin's Reckoning" from someone who supposedly knows a lot about when animation is strong and when it's weak. The opinion was that "Part 1" of that pair of episodes has the best drawing and animation of them all, along with "Heart Of Ice" (aside from the reversed colour scheme on the bat symbol in two shots).
"Robin's Reckoning, Part One" probably has the best animation every produced for the series. The amazing use of shadow, multi-layering of color, and just stunning directing and a killer script has made this a stand out episode for the series. We'll get it on Volume Two. Other episode (butnot limited to) that have served as animation standouts include "On Leather Wings," "Heart of Ice," "Two-Face, Part One," "Feat of Clay, Part Two," "Fear of Victory, "Almost Got 'Im," and "Over The Edge." With luck, we'll have all those episodes and every other Batman episode by the end of 2005.