Every time I try to download something Safari pops up, and the download is done by Safari(X10.5) and not Limewire, how can I stop this?

Are you refering to torrents or normal usage of the gnutella network?
Torrents need to be initially downloaded by your browser, then open those (filename.torrent) with LW.

If it's not torrents where your problem is .. hmm not sure. Which was installed first, LW or safari? Try deleting your LW prefs whilst LW is closed; Deleting LW Preferences folder in OSX