So, soon I will have both games for PC.

I would like to be able to use some buildings from Megaton in a Fallout: New Vegas mod and Bring some things from Fallout: New Vegas into Fallout 3, is this legal? I've read somewhere that even with both games owned legally, you still can't do it. Is this true?

Since you bought both games, what you do with them is up to you. You cannot make a mod that uses assets from a copyrighted game and than upload it on a file sharing service to be used by other people. As long as you use the mod only in your game, no one will know, will they?

Ah, ok. So as long as I don't release it, it should be fine?

There is a mod that let you play Fallout 3 from Fallout : New Vegas (A Requiem for the Capital Wasteland).

You have to have both games. Basically, you export all the info from Fallout 3 and copy them in Fallout New Vegas.

I think you can use the same technique to get objects from Fallout 3 into Fallout : New Vegas.

I can think of published Fallout mods where, say, 95% of the assets are from Fallout 3 and related DLC, while only 5% are custom built. It would be very difficult not to use any existing assets to produce a mod. For example, if the mod was simply a quest, then that uses ALL the assets in the game. Take another example, an item such as a 10mm ammo - it would be strange if we had to remake that! if what you say is correct, then it means that the majority of mods out there that one can download are breaking some kind of copyright law. Bethesda must be fully aware that this goes on.

As I understand it, Bethesda don't like it when assets are exchanged between games, for example such as Morrowind and Oblivion, or Fallout 3 and Skyrim. I'm not sure about Vegas.

According to my understanding of a mod, it modifies existing data files as they are loaded into the memory. So in order to use a mod, you must already own the original game and DLC for it to work. In which case no-one has gotten anything for free. At least that's how plugins work. I can't see any problem with this kind of mod. Are there other kinds of mods?

Most assets are transferred in New Vegas, including some FO3 DLC ones like the trogs (only the textures are missing). What is prohibited is to take something specific to a game and copy it to the other game to release, like Festus or the NCR armor.
If you try to copy an interior cell like Chrislus Building to NV many walls will be missing and don't exist in NV. Here you can't extract the missing piecs from FO3 BSA and add them to a NV mod.

But you can convert Vault 11 or vault 003 interiors to FO3 in one pass because the assets are already in FO3. You only get the vault layout though, some items will be missing like the number on the doors, some misc items ingestibles, posters or the vaultsuits. There you can't extract it from the NV bsa and add them to a FO3 mod. You have to replace them with things you have in FO3.

You can't port the gomorrah to FO3 or point lookout to NV because the parts needed are missing if you don't own the game or the DLC. You can do it for yourself but not deliver the missing pieces from one game to a mod dedicated to the other game.
It is exactly the same as Oblivion, Morrowind or Skyrim to NV. If you own the game and keep the mod for yourself you can convert everything. I use several meshes converted from Oblivion to FO3 but I don't release the mod.

But if you intend to share what you've done, then so long as the mod only modifies existing installed files, and adds non-copyright content (for exampel your own sounds and textures), then you're ok, I believe?

I am not bethesda staff but this is how I understand it too.
As long as you have the resource delivered with the game itself (like super mutant behemoth mesh present but not used in NV) you can create a texture and use the Behemoth creature in a mod for NV but not import a swampfolk in NV because the mesh and texture are not initially in the game.