Here is a list of bobbleheads that may become unobtainable and how to avoid that happening. All other bobbleheads can be obtained at any point in your playthrough, including after completing every available mission.
Medicine - on your father's desk in vault 101
*** Spoiler - click to reveal ***Make sure you get this one before you leave vault 101, failing that, you can re-enter vault 101 in the quest, "trouble on the homefront", which becomes available after completing the "waters of life" quest.
Energy weapons - inside Raven Rock
*** Spoiler - click to reveal ***Make sure you get this before speaking to the computer (if you choose to trick the computer into blowing up the compound) otherwise you cannot get back up to level 2 where the bobblehead is located.
Strength - Lucas Simms' house in Megaton
*** Spoiler - click to reveal ***If you choose to blow up megaton in the quest "power of the atom", make sure that you grab the bobblehead from his house before doing so. (His house is locked, but can be entered via the roof, or you can kill/pickpocket Lucas Simms for the key)
Repair - Evan King's house in Arefu
*** Spoiler - click to reveal ***Can be made unobtainable if you try to force the lock to Evan King's house and fail, breaking the lock. Note that the infiltrator perk, if chosen, will give you a second and final chance.
I hope this prevents some achievement hunting disaster for some people :)
If you've encountered any other problems like these, please comment below so I can add them to the guide :)