Bubonic Plague, probably.
As far as I know, bubonic plague has been "wiped out" of the globe....
Not sure about it, though.
The "yellow fever" originates when a flu virus in large chicken populations mutates into a kind of virus that can affect humans.
Cholera and STD's would be the major problem in a wasteland post apoc-world... I lived in southeast Mexico for ten years, as a kid. I remember a lot of government pamphlets, special "classes" at school and ads on the tv. In fact, it's pretty easy to catch cholera in a "non hygienic" environment, and I doubt a post apoc wasteland would be a place full of water purification plants and antiseptic factories.
As for the STD's... I don't think I have to explain the flower and bees thing, do I?
Pope Viper wrote
You get a standard flu, gets some nice irradiation, and boom, you've got a much more difficult customer to deal with.
In fact, the mutations in Fallout were due to the different strains of FEV virii, the mutated geckoes, ants etc. were supposed to be caused by large amounts of FEV released in the earth's atmosphere, after the facility that developed it was hit by an ICBM.
(Gives a new meaning to the word "Fallout", eh?)
In any case, most of humanity, and thus, most of humanity's virus/bacteria hosts were submitted to a thermonuclear city-cleansing programme. I doubt that many diseases would survive a full scale nuclear war.
The Vault Dwellers probably had some kind of "purification" process before entering the vaults ( 70's underground virus-proof complex movie reference )
Having diseases in both fallouts could be interesting to a certain point, fully applying the FEV rules to virii would result in a macrovirus that wiped out humanity ( except the vault dwellers) in the next year or so after the bomb...