Recommended way to deal with locally-compiled apps

[CB]

CB wrote:

> How do you guys deal with apps you choose to compile and/or install 
> yourself? (particularly where there are ubuntu packages available but 
> you want/need a more recent version).
>
> Is there a standard place to put them, good practise to avoid 
> conflicts with packaged stuff, etc?
>

Supplementary to this: what happens if I overwrite parts of an existing 
package with newer files? Will that cause problems for future apt-get 
upgrades of the package? An example is backuppc. It has an ubuntu 
package which is a bit out-of-date. It's only perl scripts, so it would 
be easy to just plonk the new scripts in the appropriate directory. Is 
this a bad idea for any reason?