I thought they were usually known by the version letter, such as
"Emil" for the 109E, "Gustav" for the 109G, etc.

Not nearly as common as the 1970s books made it seem - most '109 guys' didn't
go for the nicknames in general. "Me", "Focke-Wulf", and "Dora" are the only
three nicknames that I routinely encountered during interviews with WWII German
aviators. I know that much is made of "Emil" and "Gustav", but most of the
guys didn't think variations to the basic airframe all that important. A 109
pilot usually said he flew 109s, not an Emil or a Gustav. A large percentage
of the 109 pilots flew exclusively in the latter stages of the war, so all they
ever knew was the G-series (K-4s were quite rare). No pilot I have talked to
has identified his aircraft by subtype - although the nightfighter 109 guys
flew highly modified Bf 109 G-10s and G-14s, none of the guys in Jotka 300
seemed to know/care which of the variants they drove around the sky.

v/r
Gordon
Stormbirds.com/recon