The php-5.0.* eclass (php5-sapi-r2.eclass) hard-depends on mysql-4.0.*. I can't see a reason why php5 shouldn't work together with mysql-4.1.* (it does here), so please change that to >=dev-db/mysql-4.0.0.
Hanno, this was discussed in 95632; I was told that it would break the tree wrt thttpd ebuild. I also find this unfortunate and the way around this block/limitation is really cumbersome. :(
*** This bug has been marked as a duplicate of 95632 ***