A lot of mods that include .esm files say that the .esm MUST be placed directly after the Oblivion.esm, and if not, certain parts of the landscape will not appear. while this is fine if you only want to use one of these mods, using more than one gets extremely annoying.:
If we could create a program that took the .esm files that needed to be loaded at the same time, and merge those into one .esm file.
There is a program on TESNexus that i found, but it did not work.

Anyone know how this could be done?

Tools already exist to resolve these things...
http://www.uesp.net/wiki/Oblivion:Oblivion#Mods is most useful. Do read there a bit, please

Using mods is made much easier by utilizing programs like http://www.tesnexus.com/downloads/file.php?id=2097 and http://www.tesnexus.com/downloads/file.php?id=22368. If you don't have either of those, I'd suggest getting them. They will make your modding experience MUCH easier.

Also, make sure to read the instructions for each program so you know how to use it.

ihave those, but that doesnt solve the problem.
eg.

Mod1.esm must be loaded directly after Oblivion.esm, if not, the mod will not work. Thats obvious to solve, just put Mod1.esm directly after and evberything will be fine.
Mod2.esm must be loaded directly after Oblivion.esm, if not, the mod will not work. Both mods cant be second in the load order, one will have to be third and will invariably, not work, i need a program that makes Mod1+Mod2.esm so they can both be in the same spot, as a single file.

Which mods need to load directly after Oblivion.esm? I don't think I've ever seen that requirement. :unsure:

You can use TES4Gecko to convert masters to plugins, then merge them and convert the product back to a master.

I'm not entirely sure on the necessity of having certain mods loading second, I know that if you don't load them early then the land disappears, but it would be interesting to know how other worldspace mods get around that problem and don't have to load early. I'm not convinced that it can't be solved simply by making the mod a certain way, or else every new worldpace mod would require this, and they don't.

Gates To Aesgaard 2 is the only mod I know that has to load early, I remember there being another (perhaps Underdark?) that also required it, but then they updated it and let the BOSS team know that it no longer had to load early. If memory serves, it was acronymed TRoN or something similar. Hence my suspicion that it's not unavoidable.

Just load them one after another for now, and see what happens.

This is total nonsense, there is no such mod that requires such a thing. I have mulitple esms loaded after my oblivion.esm and they all work fine

Actually, Gates To Aesgaard 2's esm does need to load early to avoid missing land. I'm not sure why, or if it specifically has to be loading second, but it does.

As I've said above though, I think this is definitely avoidable, considering the number of worldspace mods there are that don't have this requirement, but that's just how GTA2 is built.

It would help clear things up if the OP specified which two mods they were talking about.

There are several mods which need to have their ESM loaded immediately after Oblivion.esm for their LOD to be visible.

As has already been mentioned by wrinklyninja, you need TES4Gecko. However, you need to use the "Move Worldspaces" function, not the "Convert to Master" function wrinklyninja suggested.

I think what the OP is talking about is the VWD landscape of mods with custom worldspaces. If you don't move worldspaces in TESGecko the mod needs to load first after Oblivion.esm or the distant landscape won't show up. The only mod I know of that has this problem is 'The Lands of Solstheim Vvardenfell Mournhold'. There are probably more though. Not sure why their authors didn't move worldspaces since there is no reason not to. I guess they simply didn't know about it.

another one that needs this is SoVvM,
GTA2 is one that i am searching for the mod, but due to my terrible internet, the download cuts out after 5-7 mins, so i need to get them to upload the actual mod to TESNexus.
I tried the Gecko thing but it keeps crashing.

When i try to do anything to SoVvM.esm it gets to 69% and then a huge error box comes up.

Wouldn't http://www.tesnexus.com/downloads/file.php?id=15781 solve that problem?

@ Vorians: Cheers for the explanation. I might get ahold of The Priest to see about getting permission to release another patch update to GTA2 to address this, if just the esm needs altering it should be possible.

Ah, OK, those are just about the only kind of mods I've never used.

if its not too much to ask, could someone do the move worldspaces on Gecko on SoVvM.esm? and upload to a file hosting site. my computer fails to do it.

No. That deals with objects, buildings, etc, anything with a _far.nif file. Landscape LOD is an entirely different beast.