It is very difficult to keep track of a list of "working applications". However, most of the normal Internet applications are supported, such as WWW browsing (Netscape, MSIE, etc.), FTP (such as WS_FTP), TELNET, SSH, RealAudio, POP3 (incoming email - Pine, Eudora, Outlook), SMTP (outgoing email), etc. A somewhat more complete list of MASQ-compatible clients can be found in Section 6.3 in this HOWTO.
Applications involving more complicated protocols or special connection methods such as video conferencing software need special helper tools.
For more details, please see the Linux IP masquerading Applications page.