Both dev-python/pysqlite-1.0.1 and dev-python/pysqlite-2.3.1 were installed. Likewise, both dev-db/sqlite-2.8.16-r4 and dev-db/sqlite-3.3.5-r1 were installed as dependencies. In /var/lib/portage/world, there was only dev-python/pysqlite (without version number). emerge --depclean removed dev-db/sqlite-2.8.16-r4, while keeping obsolete dev-python/pysqlite-1.0.1 installed and breaking it's dependency at the same time.
What version of sys-apps/portage? There's a completely new depclean in >=portage-2.1.1_pre5-r2 that is much safer than the old one.
Portage 2.1-r2 (default-linux/x86/2006.0, gcc-3.4.6, glibc-2.3.6-r4, 2.6.15.7-ubuntu1-tiger-initrd i686)
It probably works fine with the new depclean. If you'd like to test it, 2.1.1_rc1 should be safe to use since we're nearing a final release and not making any more invasive changes.
