ORIGINAL: Stelteck
What you need to evacuate 100% is the IL-2 factory of voronev when the time come. Others are not so usefull.
Quite strong generalization
My guideline has been:
Khimki, Li-2: save at least 1, preferably more
Khimki, Li-2VV: not really needed, kind of useless bomber
Moscow, 2x Mig-3: save 1 or more of both, they'll upgrade to IL-2 factories
Moscow, Pe-3: save at least 1 at the last moment, low build limit and your only nightfighter (check the wiki link, it wasn't actually that good at operating in the dark

)
Moscow, IL-10: save 1 to bomb the hell out of Berlin in 1945
Moscow, Yak-6: not really needed if you spare Pe-2R, save 1 if you do heavy recon
Moscow, Pe-2: not necessary if you don't use medium distance BAPs, save 1 to double production
Moscow, Yak-7A: save 1 to increase fighter production later (Yak-7B=>Yak-9M)
Moscow, U-2VS: not necessary, I think they're great for night bombing, but you probably can manage with only the eastern factories
Moscow, IL-4: save 1 for strategic bombing
Moscow, Pe-2R: save 1, best recon craft
Taganrog, LaGG-3 '11', save 1 for later fighters with good firepower
Kharkov, Su-2: not really needed, stops production early
Voronezh, IL-2: Save them, at this point you should have spare railcap so can save more than 1
Voronezh, IL-10: save 1 to bomb the hell out of Berlin in 1945
Moscow, 2x BM-13: save 1 or more of both to keep rocket production up
Moscow, T-40: save 1 or more if you think you will use light tanks (tank brigades & corps in '42-'43)
Leningrad: BA-10, not needed
Leningrad: KV-1, save 1 for KV-1s production later
Leningrad: T-50, save 1 to boost T-34 production later
Kharkov: T-34, save at least 1, you should have enough production unless you go tank-crazy
Voronezh, 2x BM-13: save 1 or more of both to keep rocket production up
Tambov, GAZ-MM: not really needed, save 1 if you can afford
Kolomna, GAZ-MM: not really needed, save 1 if you can afford