GroupCalendar will remind you when transmute and cloth-making cooldowns
are nearly ready.

Yes, it's called StomachSounds 2.0
Turn down your speakers and you'll be auto-informed by your stomach
after 17 hours.

for taking notes there's Omnibus as already suggested.

for the cooldown stuff, you might want to search around for cooldown
adds, there are at least 2 I've used (but have forgotten the name).

Urs

No reminders, but Cosmos includes NotesUNeed for attaching notes to people.
Cartographer has a system for attaching notes to coordinates, and there's a
rich set of other addons that piggyback on Cartographer.

What I need is an addon that dings when my paladin seal runs out, as I tend
to miss it when my buff list is cluttered and I'm watching for other procs.
And perhaps an alarm for just before a mob breaks to run, so I can switch
judgements.

Well its not an in-game addon but I use a stupid little program called
Chameleon Clock. I have things I need to always do (like get my kid off the
bus) and it pops up a little note on the screen pretty strongly. Usually it
pops up in front of anything Im doing but for WoW it pops up behind the
game but has controls in the game. I have to click that part of the screen
which drops the game to the bar, then I click to close the reminder, then
click back into the game. I can also have it run something else like
popping up a picture or playing a sound.

It has a ton of timer settings. Like once, every hour, or 2 or 4, just on
weekdays, etc. I have popups for most of my chores and appointments.

The fact that its outside of WoW might be a good thing. If you start to
rely on it like I do then it will continue to work for your next game also.
http://www.softshape.com/software/desktop/chamclock/features/

Gandalf  Parker