Please feel free to add to the list or correct me:

AIRTRAN (especially good for ATL and FL based flyers):
1. Change fee $50
2. Biz-Class upgrades for $35
3. 3 rountrips in coach to get 1 free (pay with AMEX)
4. Stand-by for free
5. 6 roundtrips in coach to get 1 free from ATL to anywhere in 48US on Delta- pay with AMEX (get the miles too).

SOUTHWEST:
1. No change fee
2. Stand-by: pay full fare (max $299 each way), but no change fee and entire value of ticket can be applied.
3. 4 roundtrips to get 1 free (buy online)
4. Southwest has pretty roomy, leather seating- even though no 1st class

AMERICA WEST:
1. $100 change fee
2. Stand-by for no extra charge
3. 3000 bonus miles for each online booking- thus with about 4 rountrips, you get 1 free (their award is 20K miles).
4. Max fare is about $400-500 OW, even walk-up.

Also to be considered: ATA (Chicago-Indianapolis), Frontier (Denver), JetBlue (JFK-OAK-LGB), Spirit...