MailTags and MailActOn are a godsend: they've actually made me start using iCal again. And with the ToDo list in iCal, you can see the todo, then click on the URL to go to the email which spawned it, as well as using the Next Action description as the name of the email/ToDo. I love it.

For the handwriting thing, I hate the crossed-out messiness, so I went with stickies. I work from home, so I'm here except when I'm with a client, so I can leave a manila folder with my NA stickies, neatly ranked, open all the time. It helps because
(a) I take 'em off when they're done, so I don't get Teh Messy and I get a nice pile of done things to gloat over;
(b) I can rearrange them as many times as I like;
(c) it's great when I do a dash, because I just peel off the five stickies and go for it;
(d) it's easy to add another NA;
(e) it's got that fun Lego feel that makes me feel like a kid. ;)