The FONA 3G adds 3G support but since it is a completely different chipset than the FONA 800/808 (Qualcomm not Mediatek) there are some significant differences between the two types of modules.

This is not an exhaustive list!

SMS

SMS's are indexed differently

FONA 800 & 808 start at 1 (one) where as the FONA 3G starts at 0 (zero)

SMS sending extra lines

After sending an SMS using AT+CMGS, the FONA 3G returns two sets of CRLF's that do not appear with the FONA 800 or 808.

SMS # query reply is different

If you request the # of SMS's on the SIM module with AT+CPMS? the FONA 800 & 808 reply starts with +CPMS: "SM_P" whereas the 3G starts with +CPMS: "ME"

Voice Calls

The hanging up command is ATH0 on the FONA 800 and 808 and ATH on the FONA 3G. You'll also have to send the FONA 3G a AT+CVHU=0 command to tell it to listen for the ATH command (it will say 'OK' but not actually hang up)

Misc

Battery voltage measurement with AT+CBC returns a 4-digit voltage in mV on the FONA 800 and 808. On the FONA 3G it's a floating point number in volts.

GPS

GSMLOC (location via triangulation of nearest cell towers) is supported by the FONA 800 and 808 but not 3G