They can co-exist quite well actually.
At one point I had:
SQL Server 2005 (default instance)
SQL Server 2000 (named instance)
and
SQL Express (\SQLExpress named instance) all running on my machine all at once.
(That's the only caveat... SS 2000 and SS 2005 can't both be default instances, one will be, the other will have to be a named instance - otherwise everything works fine...)
Oh, and if you're trying to move DBs from SS 2000 to SS 2005, I'd suggest backing them up and restoring them on to the new server - works fine, seems to encounter less issues down the road.