im going to post this because google brought me here and there was no answer. Now, i have an answer so i will share....

my agent also disappeared from an install of SQL 2005. The reason is not known for 100% sure, but i believe it was from a SQL 2008 upgrade that was rolled back to SQL 2005. I could be wrong, but I did in fact end up with a perfect SQL engine and no agent. The solution was to recreate the service like this;

C:\>sc create SQLAgent binPath= "C:\Program Files\Microsoft SQL Server\MSSQL.1\MSSQL\Binn\SQLAGENT90.EXE" type= own start= auto depend= netbios

after i started the newly created service, my SQL jobs started working again without issue. (i also changed the account that runs the service from "local account" to a domain admin account)