The traditional method for checking the version of SQL Server installed is to query the value of the @@VERSION function, but if you have only have SSIS installed, you need a SSIS specific method. A very simple method is to check the File Version of the SSIS Service, C:\Program Files\Microsoft SQL Server\90\DTS\Binn\MsDtsSrvr.exe. Right-click the file and select Properties. On the Version tab check the File Version property and compare with the table below. RTM shows 9.00.1399.00, SP1 shows 9.00.2047.00
Strictly speaking the MsDtsSrvr.exe may not always be updated with a service pack or patch, so this version may reflect an older level. An alternative method is to check the registry HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Microsoft SQL Server\90\DTS\Setup, values Version and PatchLevel which give the service pack and hotfix level respectively. Current values are given in the table below.
Another place you can check the version of SSIS is through the designer, Visual Studio aka BIDS. See the BIDS page for an example, notice the version is shown in the Product Details box. This raises the point of workstation machines, do not forget to patch you clients. It is no good having a great server with all the fixes on if your tools and designers are out of date.