Also, if possible could you send the apt.conf file and sources.list that you use? Here is the log I get when I run apt-get update:
Get:1
http://ruslug.rutgers.edu apt/fedora/2 release [505B]
Get:2
http://ftp.upjs.sk 2/i386 release [1129B]
Get:3
http://sunsite.informatik.rwth-aachen.de ftp/pub/Linux/fedora/fedora/2/i386 release [2204B]
Get:4
http://mirrors.kernel.org fedora/2/i386 release [2204B]
Get:5
http://dries.studentenweb.org apt/fedora/fc2/i386 release [482B]
Get:6
http://newrpms.sunsite.dk redhat/en/i386/fc2 release [528B]
Get:7
http://rpms.xcyb.org i386 release [795B]
Get:8
http://download.fedora.us fedora/2/i386 release [2204B]
Ign
http://mirrors.sunsite.dk free release
Get:9
ftp://apt.kde-redhat.org fedora/2 release [1454B]
Get:10
http://apt.sw.be redhat/fc2/en/i386 release [438B]
Get:11
http://ayo.freshrpms.net fedora/linux/2/i386 release [1819B]
Get:12
http://rpms.xcyb.org i686 release [795B]
Get:13
http://ftp.upjs.sk fedora/2/en/i386 release [1503B]
Get:14
ftp://apt.kde-redhat.org fedora/all release [1471B]
Ign
http://gstreamer.freedesktop.org fedora/2/i386 release
Get:15
ftp://apt.kde-redhat.org kde-redhat/2 release [1176B]
Get:16
ftp://apt.kde-redhat.org kde-redhat/all release [1485B]
Fetched 20.2kB in 1s (15.9kB/s)
Hit
http://ruslug.rutgers.edu apt/fedora/2/macromedia pkglist
Hit
http://ruslug.rutgers.edu apt/fedora/2/macromedia release
Hit
http://ayo.freshrpms.net fedora/linux/2/i386/core pkglist
Hit
http://ayo.freshrpms.net fedora/linux/2/i386/core release
Hit
http://ayo.freshrpms.net fedora/linux/2/i386/freshrpms pkglist
Hit
http://ayo.freshrpms.net fedora/linux/2/i386/freshrpms release
Hit
http://ayo.freshrpms.net fedora/linux/2/i386/os pkglist
Hit
http://ayo.freshrpms.net fedora/linux/2/i386/os release
Hit
http://ayo.freshrpms.net fedora/linux/2/i386/updates pkglist
Hit
http://ayo.freshrpms.net fedora/linux/2/i386/updates release
Hit
http://ayo.freshrpms.net fedora/linux/2/i386/core srclist
Hit
http://ayo.freshrpms.net fedora/linux/2/i386/freshrpms srclist
Hit
http://apt.sw.be redhat/fc2/en/i386/dag pkglist
Hit
http://apt.sw.be redhat/fc2/en/i386/dag release
Hit
http://ftp.upjs.sk 2/i386/stable pkglist
Hit
http://ayo.freshrpms.net fedora/linux/2/i386/os srclist
Hit
http://ayo.freshrpms.net fedora/linux/2/i386/updates srclist
Hit
http://gstreamer.freedesktop.org fedora/2/i386/deps pkglist
Ign
http://gstreamer.freedesktop.org fedora/2/i386/deps release
Hit
http://gstreamer.freedesktop.org fedora/2/i386/gst pkglist
Ign
http://gstreamer.freedesktop.org fedora/2/i386/gst release
Hit
http://sunsite.informatik.rwth-aachen.de ftp/pub/Linux/fedora/fedora/2/i386/os pkglist
Hit
http://sunsite.informatik.rwth-aachen.de ftp/pub/Linux/fedora/fedora/2/i386/os release
Hit
http://sunsite.informatik.rwth-aachen.de ftp/pub/Linux/fedora/fedora/2/i386/stable pkglist
Hit
http://sunsite.informatik.rwth-aachen.de ftp/pub/Linux/fedora/fedora/2/i386/stable release
Hit
http://sunsite.informatik.rwth-aachen.de ftp/pub/Linux/fedora/fedora/2/i386/updates pkglist
Hit
http://sunsite.informatik.rwth-aachen.de ftp/pub/Linux/fedora/fedora/2/i386/updates release
Hit
http://dries.studentenweb.org apt/fedora/fc2/i386/dries pkglist
Hit
http://dries.studentenweb.org apt/fedora/fc2/i386/dries release
Hit
http://dries.studentenweb.org apt/fedora/fc2/i386/dries srclist
Hit
http://rpms.xcyb.org i386/stable pkglist
Hit
http://rpms.xcyb.org i386/stable release
Hit
http://rpms.xcyb.org i686/stable srclist
Hit
http://rpms.xcyb.org i686/bleeding srclist
Hit
http://newrpms.sunsite.dk redhat/en/i386/fc2/newrpms pkglist
Hit
http://newrpms.sunsite.dk redhat/en/i386/fc2/newrpms release
Hit
http://newrpms.sunsite.dk redhat/en/i386/fc2/newrpms srclist
Hit
http://gstreamer.freedesktop.org fedora/2/i386/deps srclist
Hit
http://gstreamer.freedesktop.org fedora/2/i386/gst srclist
Hit
http://mirrors.kernel.org fedora/2/i386/os pkglist
Hit
http://mirrors.kernel.org fedora/2/i386/os release
Hit
http://mirrors.kernel.org fedora/2/i386/updates pkglist
Hit
http://mirrors.kernel.org fedora/2/i386/updates release
Hit
http://mirrors.kernel.org fedora/2/i386/stable pkglist
Hit
http://mirrors.kernel.org fedora/2/i386/stable release
Hit
http://mirrors.kernel.org fedora/2/i386/os srclist
Hit
http://mirrors.kernel.org fedora/2/i386/updates srclist
Hit
http://mirrors.kernel.org fedora/2/i386/stable srclist
Hit
http://download.fedora.us fedora/2/i386/os pkglist
Hit
ftp://apt.kde-redhat.org fedora/2/stable pkglist
Hit
ftp://apt.kde-redhat.org fedora/2/stable release
Hit
http://ftp.upjs.sk 2/i386/stable release
Hit
ftp://apt.kde-redhat.org fedora/all/stable pkglist
Err
http://mirrors.sunsite.dk free/devel pkglist
404 Not Found
Ign
http://mirrors.sunsite.dk free/devel release
Hit
http://download.fedora.us fedora/2/i386/os release
Hit
ftp://apt.kde-redhat.org fedora/all/stable release
Hit
http://ftp.upjs.sk 2/i386/stable srclist
Err
http://mirrors.sunsite.dk free/non-free pkglist
404 Not Found
Ign
http://mirrors.sunsite.dk free/non-free release
Err
http://mirrors.sunsite.dk free/devel srclist
404 Not Found
Err
http://mirrors.sunsite.dk free/non-free srclist
404 Not Found
Hit
ftp://apt.kde-redhat.org kde-redhat/2/stable pkglist
Hit
ftp://apt.kde-redhat.org kde-redhat/2/stable release
Hit
http://download.fedora.us fedora/2/i386/updates pkglist
Hit
ftp://apt.kde-redhat.org kde-redhat/all/stable pkglist
Hit
http://ftp.upjs.sk fedora/2/en/i386/at-good pkglist
Hit
ftp://apt.kde-redhat.org kde-redhat/all/stable release
Hit
http://download.fedora.us fedora/2/i386/updates release
Hit
http://ftp.upjs.sk fedora/2/en/i386/at-good release
Hit
http://ftp.upjs.sk fedora/2/en/i386/at-stable pkglist
Hit
http://download.fedora.us fedora/2/i386/stable pkglist
Hit
http://ftp.upjs.sk fedora/2/en/i386/at-stable release
Hit
http://download.fedora.us fedora/2/i386/stable release
Hit
http://ftp.upjs.sk fedora/2/en/i386/at-good srclist
Hit
http://download.fedora.us fedora/2/i386/os srclist
Hit
http://ftp.upjs.sk fedora/2/en/i386/at-stable srclist
Hit
http://download.fedora.us fedora/2/i386/updates srclist
Hit
http://download.fedora.us fedora/2/i386/stable srclist
Failed to fetch
http://mirrors.sunsite.dk/jpackage/1.../pkglist.devel 404 Not Found
Failed to fetch
http://mirrors.sunsite.dk/jpackage/1...glist.non-free 404 Not Found
Failed to fetch
http://mirrors.sunsite.dk/jpackage/1.../srclist.devel 404 Not Found
Failed to fetch
http://mirrors.sunsite.dk/jpackage/1...clist.non-free 404 Not Found
Reading Package Lists...
Building Dependency Tree...
E: Some index files failed to download, they have been ignored, or old ones used instead.
