From my CT_Mod days (which were a very long time ago) I seem to remember that CT_PlayerNotes stores notes for friends, ignores, and guildmates. If that hasn't changed, try AuldLangSyne. It does the same thing, with the added benefit of remembering your friends' info (level, race, class, guild, etc.) after they've logged off.
I'm not even sure what the value of saving player notes per-character would be... certainly you'd maintain the same thoughts about someone on the server no matter which character you were playing on. Several addons I use have recently gone to per-character settings, and I really don't understand why. For instance, Atlas - why on earth would I want different settings for different characters? I'm pretty sure if I like the "right-click for world map" feature I'm going to use it on all my characters! Extended Quest Log did the same thing, but as it's not updated too frequently, and has a lot of options I'd rather NOT spend time duplicating, I performed LUA surgery on it and made it use global settings. Every time an addon goes this route I'm more and more thankful for the profile system employed by Ace addons.
Several addons I use have recently gone to per-character settings
i know, i freaking HATE it...
i want my addons, set once, then useable on all characters.. not spend 10 hours updating or setting, resetting my setting for each character... like i have to do with ecastingbar. nice mod but pita to keep updated
The only addons I use character specific settings on is actionbars (and then only for pet classes), unitframes (only when the action bars are different), and class specific addons. With over 7 active characters, setting up each one is a royal pain. Much love for Ace's profile system... when it works ><.
Did CT have anything to say as to why the change was made?