Its extremely difficult to give specific advice without a lot more details. Normally this
would be something Tech Support could help with, but ArcGIS 9.3 moved to "Retired"
support status with the new year. You should still make the request, though.
Given your description of the state of your database, you might find it easier to copy
out the vector data into a new database (at the same release level of your ArcGIS
Desktop -- 10.0sp5 or higher), then make another database as a transition space to
copy the undamaged rasters, then detach the old database and toss the datafiles on
a USB drive (just in case).
Once your instance is stable, then you'll have some time to research transition to
modern file-based raster management techniques with ArcGIS 10.x.
- V