Hi, I'm with you 100%. I have a Droid Eris so with the stock ROM I have this feature, but I love the Froyo-based ROMs made from CyanogenMod, and this is the #1 missing feature for me. I have Weather and Toggle Widget which looks just like the Sense clock and weather on my home screen, and tapping it will take me to whatever alarm app I want, but the default alarm app doesn't have the timer (or stopwatch).
I just found this Alarm Clock Xtreme Alarm Clock Extreme - Android app on AppBrain which has all three in one. There's a free version on the market although apparently the only limitation is that you can't have the alarm repeat daily, but at least it would be nice to try.
I haven't used it yet, but maybe this will help you, too.
Edit: Okay, I don't see the timer or stopwatch, what the heck?
Ah, I see, I chose the wrong one, and apparently there isn't a free version of this one to try. Too bad. Sorry for the false alarm.