OK, after many search, trial and errors I've managed to create an .htaccess that do what I wanted (see explanations and questions after the code block):

<IfModule mod_rewrite.c>

RewriteEngine On

#1 If the requested file is not url-mapper.php (to avoid .htaccess loop)
RewriteCond %{REQUEST_FILENAME} (?<!url-mapper\.php)$

#2 If the requested URI does not end with an extension OR if the URI ends with .php*
RewriteCond %{REQUEST_URI} !\.(.*) [OR]
RewriteCond %{REQUEST_URI} \.php.*$ [NC]

#3 If the requested URI is not in an excluded location
RewriteCond %{REQUEST_URI} !^/seo-urls\/(excluded1|excluded2)(/.*)?$

#Then serve the URI via the mapper
RewriteRule .* /seo-urls/url-mapper.php?uri=%{REQUEST_URI} [L,QSA]

</IfModule>

This is what the .htaccess should do:

1. #1 is checking that the file requested is not url-mapper.php (to avoid infinite redirect loops). This file will always be at the root of the domain.
2. #2 the .htaccess must only catch URLs that don't end with an extension (www.foo.com --> catch | www.foo.com/catch-me --> catch | www.foo.com/dont-catch.me --> don't catch) and URLs ending with .php* files (.php, .php4, .php5, .php123...).
3. #3 some directories (and childs) can be excluded from the .htaccess (in this case /seo-urls/excluded1 and /seo-urls/excluded2).
4. Finally the .htaccess feed the mapper with an hidden GET parameter named uri containing the requested uri.

Even if I tested and everything works, I want to know if what I do is correct (and if it's the "best" way to do it). I've learned a lot with this "project" but I still consider myself a beginner at .htaccess and regular expressions so I want to triple check it there before putting it in production...