I have one case with a removable motherboard tray, I have had no use for the feature. The case is a tank made by Coolermaster, but is does not have good air flow, and only room for noisy 8cm fans.
All my other good cooling cases are Antec 3 Super LanBoys, 2, 300's and 1, 900.
I have had many cases over the last 15 years, the best are ones with open air flow in the front and back with 12cm fans. The fan grille shaped like a honeycomb cuts wind noise on the Antec cases.