You can use these commands to force the upgrade.

pear upgrade --force http://pear.php.net/get/Archive_Tar http://pear.php.net/get/XML_Parser http://pear.php.net/get/Console_Getopt-1.2.2
pear upgrade --force http://pear.php.net/get/PEAR-1.3.3 (use only if your PEAR is older than v1.3.3)
pear upgrade --force http://pear.php.net/get/PEAR-1.4.3
pear upgrade PEAR

Here you can see the upgrade in action (fun fun fun).

[root@linux ~]# pear upgrade --force http://pear.php.net/get/Archive_Tar http://pear.php.net/get/XML_Parser http://pear.php.net/get/Console_Getopt-1.2.2
downloading Archive_Tar-1.3.2.tgz ...
Starting to download Archive_Tar-1.3.2.tgz (17,150 bytes)
......done: 17,150 bytes
WARNING: channel "pear.php.net" has updated its protocols, use "channel-update pear.php.net" to update
downloading XML_Parser-1.2.8.tgz ...
Starting to download XML_Parser-1.2.8.tgz (13,476 bytes)
...done: 13,476 bytes
downloading Console_Getopt-1.2.2.tgz ...
Starting to download Console_Getopt-1.2.2.tgz (4,252 bytes)
...done: 4,252 bytes
Did not download optional dependencies: pear/XML_RPC, use --alldeps to download automatically
warning: pear/PEAR dependency package "pear/Console_Getopt" downloaded version 1.2.2 is not the recommended version 1.2.3
downloading PEAR-1.7.1.tgz ...
Starting to download PEAR-1.7.1.tgz (302,377 bytes)
...done: 302,377 bytes
upgrade ok: channel://pear.php.net/PEAR-1.7.1
PEAR: Optional feature webinstaller available (PEAR's web-based installer)
PEAR: Optional feature gtkinstaller available (PEAR's PHP-GTK-based installer)
PEAR: Optional feature gtk2installer available (PEAR's PHP-GTK2-based installer)
upgrade ok: channel://pear.php.net/Console_Getopt-1.2.2
upgrade ok: channel://pear.php.net/XML_Parser-1.2.8
upgrade ok: channel://pear.php.net/Archive_Tar-1.3.2
To install use "pear install pear/PEAR#featurename"
[root@linux ~]# pear upgrade --force http://pear.php.net/get/PEAR-1.4.3
downloading PEAR-1.4.3.tgz ...
Starting to download PEAR-1.4.3.tgz (276,859 bytes)
.........................................................done: 276,859 bytes
WARNING: channel "pear.php.net" has updated its protocols, use "channel-update pear.php.net" to update
Did not download optional dependencies: pear/XML_RPC, use --alldeps to download automatically
downloading Console_Getopt-1.2.3.tgz ...
Starting to download Console_Getopt-1.2.3.tgz (4,011 bytes)
...done: 4,011 bytes
upgrade ok: channel://pear.php.net/Console_Getopt-1.2.3
upgrade ok: channel://pear.php.net/PEAR-1.4.3
PEAR: Optional feature webinstaller available (PEAR's web-based installer)
PEAR: Optional feature gtkinstaller available (PEAR's PHP-GTK-based installer)
PEAR: To install optional features use "pear install pear/PEAR#featurename"
[root@linux ~]# pear upgrade PEAR
WARNING: channel "pear.php.net" has updated its protocols, use "channel-update pear.php.net" to update
Did not download optional dependencies: pear/XML_RPC, use --alldeps to download automatically
downloading PEAR-1.7.1.tgz ...
Starting to download PEAR-1.7.1.tgz (302,377 bytes)
..............................................................done: 302,377 bytes
upgrade ok: channel://pear.php.net/PEAR-1.7.1
PEAR: Optional feature webinstaller available (PEAR's web-based installer)
PEAR: Optional feature gtkinstaller available (PEAR's PHP-GTK-based installer)
PEAR: Optional feature gtk2installer available (PEAR's PHP-GTK2-based installer)
To install use "pear install PEAR#featurename"

This article is based entirely from this PEAR Bug posting:
PEAR :: Bug #12990 :: Issues with PEAR Upgrade News Item from 1/3/08