Defense in depth is always better than not, at least as far as security goes. Using WPA (encryption) and MAC filtering is better than one or the other by themselves. However, WPA is far better than MAC filtering if you want to use one or the other. WPA fixes many of the problems with WEP and I am not aware of any quick way to crack WPA if it is used with TKIP, and even more so if it is used with AES (your hardware has to support this).
To sum it up, I would NEVER just used MAC filtering with encryption because on an unencrypted wireless network, picking your "approved" MAC addresses out of the air is trivial for an attacker who can then change their's to match your approved one, thus allowing them complete access to your network. Contrast this with WPA where the attacker needs to know the encryption key and, as far as I know, the algorithm (whether TKIP or AES) is designed not to reveal the key in any way.