It's so hard to choose just one! So I'm going to cheat and name a favorite from each album:
"Earlybird" - I just love the vibe of this song; the harmonies, the chord progression, it has that perfect country-rock feel to it.
"Doolin-Dalton/Desperado (Reprise)" - this is especially hard because I really love Desperado and I think this is my favorite because it does reprise the two most memorable themes of the concept. But "Bitter Creek" is a close second.
"Good Day in Hell" - As I noted, On The Border is my favorite album, I think it works the best as an album and this song edges out the title track only just slightly. But it cracks me up, I think it's a great example of the kind of songwriting partnership Don and Glenn had in terms of the humor and their musical affinity.
"After The Thrill Is Gone" - Don was/is totally prescient in many ways but perhaps none so much as this song: in life, in love, in music. And their vocals are gorgeous, ye gods.
"New Kid In Town" - this was a toughie too but I think it's Glenn's finest moment and just a perfect song.
"Those Shoes" - brilliant social satire/commentary (even an unlikely feminist credo of sorts) and a totally badass tune. But "King of Hollywood" is a close second.
"Learn To Be Still" - I know this is a song which belongs more to Don than the band, but it's beautiful and poignant.
"Long Road Out of Eden" - the prog lover in me had to choose the epic, of course.