How can I create an executable .exe PE file manually?

Nice question! I don't have much expertise on this specific question, but this is how I would start:

1. PE or ELF does not create pure machine code. It also contains some header info etc. Read more: Writing custom data to executable files in Windows and Linux

2. I assume you are looking for how does ELF/PE file hold the machine code, you can get that from this question (using objdump): How do you extract only contents of an ELF section

3. Now, if you want to know how the content part is generated in the first place, i.e. how is the machine code generated, then that's the task of the compiler's code generation.

4. Try out some resource editor like ResourceEditor to understand the exe or simply ildasm.

PS: These are mostly Unix solutions, but I am sure, PE should be doing something fundamentally similar.

I think the best way to approach it will be first try to analyze how existing PE/ELFs work, basically reverse engineering. And to do that, Unix machine will be a good point to start. And then do your magic :)

Not same but a similar question here.

Update:

I generated an object dump out of a sample c code. Now, I assume that's what you are targeting right? You need to know do you generate this file (a.out)?

https://gist.github.com/1329947

Take a look at this image, a life time of a c code.

SourceNow, just to be clear, you are looking to implement the final step, i.e. conversion of object code to executable code?

As in many of his articles, I'd say Matt Pietrek's piece about PE internals remains the best introdction to the matter more than a decade after being written.

Iv'e used "Wotsit's File Format" for years... all the way back to the days of MS-Dos :-) and back to when it was just a collection of text files you could download from most BBS systems called "The Game programmers file type encyclopaedia"

It's now owned by the people that run Gamedev.Net, and probably one of the best kept secrets on the internet.

You'll find the EXE format on this page : http://www.wotsit.org/list.asp?fc=5

Enjoy.

UPDATE June 2020 - The link above seems to be now dead, I've found the "EXE" page listed on this web archive page of the wotsit site: https://web.archive.org/web/20121019145432/http://www.wotsit.org/list.asp?al=E

UPDATE 2 - I'm keeping the edit as it was when I added the update erlier, thanks to those who wanted to edit it, but it's for a good reason I'm rejecting it:

1) Wotsit.org may at some point in the future come back online, if you actually try visiting the url, you'll find that it's not gone, it does still respond, it just responds with an error message. This tells me that someone is keeping the domain alive for whatever reason.

2) The archive links do seem to be a bit jittery, some work, some don't, sometimes they seem to work, then after a refresh they don't work, then they do work again. I remember from experience when wotsit was still online, they they had some very strange download/linking detection code in, and this probably caused archive.org to get some very wierd results, I do remember them taking this stance because of the huge number of 3rd party sites trying to cash in on their success, by pretending to be affiliate's and then direct linking to wotsit from an ad infested site.

Until the wotsit domain is removed entirely from the internet and not even the DNS responds, then would be the time to wrap everything up into single archive links, until then, this is the best way to maintain the link.