Like many others, we had Sharepoint Portal Server 2003 and SQL 2000 Reporting Services on the same server. Searching the Internet and install guides mentioned nothing about it being a problem but after I upgraded to MOSS 2007 SQL 2000 Reporting Services was dead. After digging in, the problem is that SQL 2000 Reporting Services runs under .NET 1.1 and the key is it has to run under the "Default Web Site" in IIS. MOSS 2007 upgrades the "Default Web Site" to .NET 2.0. That causes all sorts of problems for SQL 2k RS. A call to Microsoft came up with no workaround. I'll give more details on the specifics if anyone is interested, but in short...it won't work.
So what's the fix? The fx is to upgrade to SQL 2005 Reporting Services. The good news is you don't have to upgrade Sharepoint to SQL 2005. You can, but if you where like me and in a hurry to get SQL RS going you probably want a little more time to plan for that process. The way to do it, is to first backup you SQL 2000 RS DB's and then simply insert your SQL 2005 CD. Don't select any other option but Reporting Services and let is upgrade the default instance. This will upgrade the Reporting Services engine and upgrade the web site to .NET 2.0 and that will play quite nicely with MOSS 2007. Hope this helps someone out.