Eclipse with SVN (e.g. Subclipse plugin) looks in three places for a proxy server configuration:
The first place (NOT for SVN internet connections):
-> Windows -> Preferences -> General -> Network Connections
The proxy servers that are shown here are…
… added by default by eclipse (Proxy entries: HTTP, HTTPS, SOCKS; Proxy bypass: localhost, 127.0.0.1).
The second place is the Internet Explorer. If you go to Extras->Internet Options->Connections->LAN Options->Proxy Server in Internet Explorer, you can add a proxy server manually. Eclipse/Flash Builder also adds these manual proxy settings to its own connections.
The rest of the connections in Eclipse/Flash Builder are added manually by the user.
The third place (for SVN internet connections):
SVN stores its proxy in a configuration file. If you look for it in Windows XP here is a good manual. If you look for it under Windows 7 (or Vista?) go to C:\Users\MyUserId\AppData\Roaming\Subversion\servers. http-proxy-host and http-proxy-port control the proxy used by SVN (e.g. subclipse in eclipse).