What do you mean 'can sql server agent run in Windows98'?
SQL Server Agent is part of any SQL Server install. So if you can install SQL Server, then the Agent service can run also.
However, according to Microsoft's web site, these are the only two versions of SQL Server that can run on Win98:
• SQL Server 2000 Personal Edition2 and SQL Server 2000 Desktop Engine (MSDE)
Refer to: http://www.microsoft.com/sql/evaluation/sysreqs/2000/default.asp
-SQLBill