There are none that you will never be able to access, besides the higher floors of the Lavender Town Radio Tower and the 7-8 Underground Path. However, there are some that you can't access until meeting certain requirments.
-A man prevents you from going further along in Route 32 until you beat the Violet City Gym Leader and get the Togepi egg.
-The Tin Tower is blocked by Sages until you get the appropriate item to access it.
-Unlike the Girl Scouts, the RageCandyBar Man won't go away after buying their candy. You need to stop Team Rocket in Goldenrod first.
-Speaking of Team Rocket, there are parts of the Radio Tower that can only be accessed once Team Rocket has taken it over.
-Guards at the Badge Check Station will prevent you from accessing Mt Silver and Route 22 until you get all 16 badges.
-Can't get on the SS Aqua until you get the SS Ticket.
-Can't get on the Magnet Train until you get a Pass from Copycat.
There are also locations blocked by things other than human guards, such as Snorlax blocking Diglett Cave. Plus the standard HM blocks, such as Cianwood until getting Surf.
As MiniNinetales said, it's the Gen I games (and their remakes) that have the connection buildings with guards that prevent you from entering Saffron.