well i think its safe to say that i've been everywhere in the game but hopefully am wrong so those anyone know any secret place, i've discovered every marked place in the game and for unmarked place i've discovered the following
Deathclaw island
that place were several lakelurks are, its near the deathclaw island
that place near Niptin were the Rad Scorpion Queen is
that place near Camp Maccarean were the Ant Queen is
that place were the nuke is
that place were the ufo/meceneries are
that trail in Jacobstown that leads to red rock canyon
well thats about all the unmarked places that i have found just wondering if you guys might know any more

It's not secret per se since it has a marker, but have you been to the cave underneath Lake Mead? It's very beautiufl.

There's an unmarked cave that's part of the Thorn quest line.

There's quite a few caves and such all along the cliff faces. there was one that is filled with Fire Geckos, but there's really no need (that I've seen, unless there was a quest I missed) to go in it. There's no exit; just the entrance that forks in two dead-end directions, both leading to nothing but Geckos. I dont think that shows up as a marker tho. (Bootjack Cavern? If it is the cave I just mentioned, then yes. Its unmarked, according to Wiki) And there's this cannibal that lives in a different cave not far from the Gecko cave (Cannibal Johnson's Cave)