The problem is this could be a tome, but maybe it will be done in 8 parts.
1) Notes
2) iNotes
3) Domino
4) Quickr D/J
5) Sametime
6) Connections
7) Portal
edited after Bens comments to include:
8) LotusLive
Start with the obvious issues, move to more extensive problems that deal with iNotes integration, SSL, SSO, calendaring and scheduling, install