While I wouldn't do it myself, you can certainly change  the _layouts
virtual directory in IIS to point somewhere else.

Most of the system will try to go into /_layouts/LCID to get images, aspx
pages, etc. (where LCID is 1033 for English portals).

What exactly are you trying to do here? When you say "I want to modify  all
files under /_layouts/1033" are you trying to do something like a global
branding? Frankly I wouldn't bother as you have to deal with:

-215 aspx pages
-6 css files  (with about a million classes in them)
-21 javascript files (about 800k)
-7 html files
-65 gifs

Okay, so you don't have to change  everyone one of them but probably at least
150 of the aspx pages and most of the javascript. That's probably a few
hundred man hours of work (rough guess).

If you're trying for a "I want my portal to look unique" just do basic stuff
with CSS files, a custom logo, and wait for Master pages and vNext as it
will make your life a lot easier.

I have to get a perticular branding for common  files with header &
footer.
Header can be solved using alternateHeader attribute of project tag.
style can be achived applying themes. But my concern is footer.
Sharepoint does not have anything for footer(As for as i know...).
So, i have to add footer to all pages. May be some other
customization for common pages. and i dont want to change  original
files.
I am looking for some way to forward request to my own folder
for example  /_layouts/1033/demo
with out much efforts in this.
I dont have to change any functionality provided by sharepoint  as of
now may be some other customization might be required.

Check out this blog which discusses options for a custom footer:
blogs.msdn.com/.../158197.aspx

The AlternateHeader option works, but some pages (I think all the admin
pages) won't pick it up.

The other thing is to probably create  a custom area def and then you can put
whatever you want into the default.aspx. You can also edit the SMARTPGS
files that are the templates for any new Web Part Pages and add them there.

My advice, don't knock yourself out over this as I feel it's not worth the
effort to do all this. I know people will scream that there has to be a
copyright notice or something, but personally I don't think that's worth a
week of someone's time. YMMV.

mindsharpblogs.com/.../458.aspx

In the word of Willie Wonka from the original Willie Wonka and the
Chocolate Factory:
"Strike that, reverse it." (Bil did say "think") ; )

Willie also said, "A little nonsense now and then, is relished by the
wisest men."

All the admin pages will pick up the AlternateHeader option but all the
direct mode pages will not.

I do not recommend that people use the AlternateHeader option because:
1. You must manually edit all 102 pages in your custom site definition
to add the conditional logic.
2. The conditional logic is server-side code which will cause the page
to fail if it is ever unghosted (it does kinda work as unghost
protection).
3. The direct mode page version  of the conditional logic requires that
the <form> tag be moved and cannot use Server.Execute but instead use
Response.Write. This means that the header cannot itself run any
server-side code.
4. It doesn't handle the needs for an alternate footer.
5. etc.

Use one of the other approaches.

I say more in my sharepoint  Advisor article:
http://mssharepoint.advisorguide.com/doc/16799