You cannot configure a single Oracle instance to run more than one ArcGIS geodatabase (not with one ArcGIS release, nor with multiple releases). You must have multiple instances to run multiple geodatabases with Oracle (other databases can support different ArcGIS releases in each database, but only up to a certain point).
I wouldn't recommend using an application server service on a host where you'll also be running a 32-bit client (at the 9.3.1 release, either ArcGIS Desktop or ArcGIS Server) -- Instead use Direct Connect (the 32-bit Oracle client must be first in the PATH).
It is possible to run multiple Application Servers with different ArcGIS releases (I do it all the time), but it's difficult, and it isn't supported (and it once contributed to trashing one of my VMs). Playing mix-n-match with application word size on Windows hosts is a real nightmare (but trivial on Linux).
The best way to avoid trouble is to use Direct Connect and forget using application servers at all. The only supported way to run multiple application servers is to use multiple hosts (which will cost you twice as much in licensing).
Within the same Oracle instance and within the same Oracle database, you can have multiple user-schema geodatabases but one and only one SDE schema (referred to often as the master schema). In other words, you have one master geodatabase and multiple user-schema geodatabases which are essentially system-managed through the SDE schema. All of those user schemas MUST be at the same Esri release; you cannot have one user schema at 9.3.1, one at 10.0, and another at 10.1 SP1 while the SDE user schema is at 10.2. Upgrading the geodatabase will migrate all user schemas to the same version (at 10.1 and higher, the Upgrade Geodatabase tool does this automatically) and it's not possible to use multiple releases, period.