Yo uso APT en Fedora Core 3, y no tengo un archivo /etc/apt/sources.list, sino varios archivos dentro del directorio /etc/apt/sources.list.d. Te pongo su contenido, por si te sirve de ejemplo:
/etc/apt/sources.list.d/atrpms.list
# Name: ATrpms
# URL:
http://atrpms.physik.fu-berlin.de/
### Fedora Core
# rpm
http://apt.physik.fu-berlin.de/ fedora/3/en/i386 at-testing
# rpm
http://apt.physik.fu-berlin.de/ fedora/2/en/i386 at-testing
# rpm
http://apt.physik.fu-berlin.de/ fedora/1/en/i386 at-testing
### Red Hat Linux
# rpm
http://apt.physik.fu-berlin.de/ redhat/9/en/i386 at-testing
# rpm
http://apt.physik.fu-berlin.de/ redhat/8.0/en/i386 at-testing
# rpm
http://apt.physik.fu-berlin.de/ redhat/7.3/en/i386 at-testing
/etc/apt/sources.list.d/dag.list
# Name: Dag RPM Repository
# URL:
http://dag.wieers.com/apt/
### Dag RPM Repository for Fedora Core
rpm
http://apt.sw.be/ fedora/3/en/i386 dag
# rpm
http://apt.sw.be/ fedora/2/en/i386 dag
# rpm
http://apt.sw.be/ fedora/1/en/i386 dag
### Dag RPM Repository for Red Hat Enterprise Linux
# rpm
http://apt.sw.be/ redhat/el3/en/i386 dag
# rpm
http://apt.sw.be/ redhat/el2.1/en/i386 dag
### Dag RPM Repository for Red Hat
# rpm
http://apt.sw.be/ redhat/9/en/i386 dag
# rpm
http://apt.sw.be/ redhat/8.0/en/i386 dag
# rpm
http://apt.sw.be/ redhat/7.3/en/i386 dag
# rpm
http://apt.sw.be/ redhat/6.2/en/i386 dag
/etc/apt/sources.list.d/dries.list
# Name: Dries RPM Repository
# URL:
http://dries.studentenweb.org/apt/
### Fedora Core
rpm
http://apt.sw.be/ dries/fedora/fc3/i386 dries
# rpm
http://apt.sw.be/ dries/fedora/fc2/i386 dries
# rpm
http://apt.sw.be/ dries/fedora/fc1/i386 dries
### Red Hat Enterprise Linux
# rpm
http://apt.sw.be/ dries/redhat/el3/en/i386 dries
/etc/apt/sources.list.d/freshrpms.list
# Name: FreshRPMS
# URL:
http://ayo.freshrpms.net/
### Fedora Core
rpm
http://ayo.freshrpms.net/ fedora/linux/3/i386 freshrpms
# rpm
http://ayo.freshrpms.net/ fedora/linux/2/i386 freshrpms
# rpm
http://ayo.freshrpms.net/ fedora/linux/1/i386 freshrpms
### Red Hat Linux
# rpm
http://ayo.freshrpms.net/ redhat/9/i386 freshrpms
# rpm
http://ayo.freshrpms.net/ redhat/8.0/i386 freshrpms
# rpm
http://ayo.freshrpms.net/ redhat/7.3/i386 freshrpms
# rpm
http://ayo.freshrpms.net/ redhat/6.2/i386 freshrpms
/etc/apt/sources.list.d/newrpms.list
# Name: NewRPMS
# URL:
http://newrpms.sunsite.dk/
### Fedora Core
rpm
http://newrpms.sunsite.dk/apt/ redhat/en/i386/fc3 newrpms
# rpm
http://newrpms.sunsite.dk/apt/ redhat/en/i386/fc2 newrpms
# rpm
http://newrpms.sunsite.dk/apt/ redhat/en/i386/fc1 newrpms
### Red Hat Linux
# rpm
http://newrpms.sunsite.dk/apt/ redhat/en/i386/9.0 newrpms
# rpm
http://newrpms.sunsite.dk/apt/ redhat/en/i386/8.0 newrpms
/etc/apt/sources.list.d/os.list
# Name: FreshRPMS OS/updates
# URL:
http://ayo.freshrpms.net/
### Fedora Core
rpm
http://ayo.freshrpms.net/ fedora/linux/3/i386 core updates
# rpm
http://ayo.freshrpms.net/ fedora/linux/2/i386 core updates
# rpm
http://ayo.freshrpms.net/ fedora/linux/1/i386 core updates
### Tao Linux 1.0
# rpm
http://dist.taolinux.org/ tao-1.0-i386 os updates
### Red Hat Linux
# rpm
http://ayo.freshrpms.net/ redhat/9/i386 os updates
# rpm
http://ayo.freshrpms.net/ redhat/8.0/i386 os updates
# rpm
http://ayo.freshrpms.net/ redhat/7.3/i386 os updates
# rpm
http://ayo.freshrpms.net/ redhat/6.2/i386 os powertools updates
Supongo que ya sabes que las líneas que comienzan por almohadilla (#) no son tenidas en cuenta. En estos archivos .list aparecen los repositorios hasta Fedora Core 3, tan sólo tendrías que comentarlos mediante la almohadilla (#), y añadir los repositorios de Fedora Core 4 correspondientes.