I have both my iPod (Touch 4G) with iOS 6 and MacBook with 10.8.latest and I set up iCloud on both, and my contacts and calendar events appear to synch via iCloud but for some reason Notes does not.
I rarely use reminders in the iPod but I have some there, and I just checked on my Mac and all the iPod (iCloud) reminders are in reminders on my Mac, but still no iPod notes on the Mac.
I just re-checked iCloud and it shows Contacts, Calendar & Reminders and Notes checked (along with Find My Mac) but no iPod Notes, and the one note I have on the MacBook does show in my iPod Notes. I just checked it. I changed the content of that one note on the Mac and it changed on the iPod. I changed that note on the iPod and it was really cool to see it change on the Mac, but where are the rest of my iPod notes?
Oh semi-happy joy. I found out what's going on. According to http://support.apple.com/kb/HT4191?viewlocale=en_US, my iPod iOS Settings> Notes storage was "on my iPod", instead of iCloud. Once I switched it to iCloud, a new note showed up on both.
Now I have to figure out how to get the rest of the iPod notes from local to iCloud, as the article (above) says I have to "copy or transfer them to iCloud or IMAP to sync with your other devices", but it gives no directions for that or a link to the directions or what to search for to find that (so only the applicable results show up).
I thought I'd lost my notes, too. I also have an iPad mini, and noticed the notes app icon and clicked on it. What was more obvious on the iPad was that there are different accounts; in other words, it had different sets of notes saved under different email accounts.My missing notes were saved under my icloud account, although I didn't consciously ever put the notes under any separate account. They were visible when I clicked "All Notes," too. It turns out that the phone had a different account set as the default. I changed the default on the iPhone, and there they were. I took screen shots so the notes are saved in my photos, too. This was a lot easier than checking through a lot of backups. I hope that helps. I will post this on a couple of threads I see in Apple communities. I see it's a pretty common problem.