handwritten note

I think it is.

Either it's a good sign or they ran out of form rejection slips...

It can also depend on the agent. I think there are some agents more likely to handwrite a note than others. If the handwritten note was from a big-name agency that sends hundreds of rejections a week, then I'd say it's a good sign that there was something about your query/sample that the agent thought more of you than to just send a form.

Probably a good sign, unless it says "just didn't excite me".

It depends entirely on what it says.

It doesn't necessarily mean anything. Some agents hand-write "NO" on submissions and send them back. Others hand-write because they don't like to type or they can hand-write faster than typing, or because they decided to hand-write rejections on a plane or something when they didn't have their computer. It really depends on the agent's personal style. It also depends on what it says. If you get a long, heartfelt note handwritten with a fountain pen on nice stationery, it's entirely different than someone writing "NO" or "NOT FOR ME" on a slip of paper.

A rejection is a rejection is a rejection. Don't try to read too much into it. Move on to the next agent.