To generate the systray alerts for contacts signing on requires you to edit a contact's "alerts".
1) Right click on the contact you wish to have this happen to
2) Click on the Set Alerts option (or modify alerts if you already have one set up)
3) Click the appropriate notify box, comes online for example.
4) Click the "A systray-based popup alert" option
5) if you wish to have htis happen all the time, click "Save this alert"
Done! You will now be notified by the systray when that contact comes online.
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http://www.trillian.cc/help/sec-1.php?hchap=3&hsub=2&hsect=6Snowball