Would an M of N transaction be considered "unusual" or "non-standard"?
When you say "your wallet won't recognize" are you specifically referring to "listunspent" and "listtransactions", or just the balance displayed in the user interface?
Yes. Yes. All of them. Txn requiring third party sigantures are treated like someone elses transaction right now, and to spend them you need to use the raw transaction API manually.
For multisignature to get shown as an IsMine transaction we'll likely need to support that via multiwallet support, and you'll have a seperate wallet for each group of multisignature rules. So then e.g. WallWbob's balance will reflect the coins you can spend with bob's help.