Question: I am looking at uClinux system that builds the kernel with arm-linux-xxx, but builds the user apps with arm-elf-xxx.

If the apps are intended to run on linux, wouldn't it be better to build everything with arm-linux-xxx ?

Where does one set that option in the overall uClinux build config?

Answer: 
The names of the compilers don't necessarily mean anything. Depending on who built the compilers (and named them), you'll get differing results. Arguably, there is a correct name for a particular configuration, but some random compiled gcc may not be correct.

For the CodeSourcery compilers (likely the most correct names), see [their platforms page](http://www.codesourcery.com/sgpp/platforms.html) for what their naming means.
ELF is the binary format [linux and many others](http://en.wikipedia.org/wiki/Executable_and_Linkable_Format) use:

> 
> The ELF format has replaced older
>  executable formats such as a.out and
>  COFF in many Unix-like operating
>  systems such as Linux, Solaris, IRIX,
>  FreeBSD, NetBSD, OpenBSD, DragonFly
>  BSD, Syllable, and HP-UX (except for
>  32-bit PA-RISC programs which continue
>  to use SOM). ELF has also seen some
>  adoption in non-Unix operating
>  systems, such as the Itanium version
>  of OpenVMS, and BeOS Revision 4 and
>  later for x86 based computers (where
>  it replaced the Portable Executable
>  format; the PowerPC version stayed
>  with Preferred Executable Format). The
>  PlayStation Portable, PlayStation 2,
>  PlayStation 3, Wii and GP2X consoles
>  also use ELF. AmigaOS 4 and MorphOS
>  also running on PowerPC machines, use
>  ELF. On the Amiga platform the ELF
>  executable has replaced the previous
>  EHF (Extended Hunk Format) which was
>  used on Amigas equipped with PPC
>  processor expansion cards. The Symbian
>  OS v9 uses E32Image[3] format that is
>  based on ELF file format.
> 
> 
> Most Sony Ericsson (for example, the
>  W800i, W610, K790, etc.), some Siemens
>  (SGOLD and SGOLD2 platforms: from
>  Siemens C65 to S75 and BenQ-Siemens
>  E71/EL71) and Motorola (for example,
>  the E398, SLVR L7, v360, v3i and all
>  phone LTE2 which has the patch apply)
>  phones can run ELF files through the
>  use of a patch that adds assembly code
>  to the main firmware (Known as the
>  ELFPack, in the underground modding
>  culture).
> 
> 
>