On Friday, when I picked up my Pre, I was sure that I was going to miss all my apps. Now it is Monday night (ok Tuesday Morning) and I'm trying to remember which apps those were, besides some of the games. It is harder than I thought it would be.
CallRec was cool for both Voice Memos and for not having to write down things during a call. Just go back an listen.
I do miss one handedness, coming from Treo 600, 650, 700, 755p. But I am getting better at thumb flipping and starting. I can now one hand start apps and close them pretty well. It turns out to be faster than with the Treo.
A good eBook reader. MobiPocket is really no more, since Amazon decided to buy them to kill them and force the Kindle everywhere. No WebOS version of that. So I'm really wanting a good auto scrolling eBook reader. Might start working on this if I don't see anyone else taking it up in the next few weeks. I'm sure I'll get back to reading more eBooks once the blast of new media available subsides.
Snapper mail had nice keyboard navigation. O for next, I for previous, D to delete and go to next message. This would really speed up reading through email. I might hack the standard email client for that functionality.
Oh, yes. How can we forget USB Modem. However, half or more of the things I had to tether for are now possible on the Pre. This need isn't gone, but severely reduced.
The speed of the Pre and instant updates for Twitter, Email, SMS and clean, quick handling of these makes me just want to help getting those missing things on the Pre.
One thing I noticed while taking a phone call in the car today is the improvement of the mic over the Treo. More than once, my wife asked if I was there. The Treo used to ramp up amplification if you weren't talking, so ambient noise came through really bad. I was driving my '96 Maxima with 282k miles on it, so there is a little ambient noise there.

She said it was almost dead silent on the other end when I wasn't talking. That is a good improvement.
Edit: Almost forgot about downloading from the browser, along with opening Zip files if needed. Almost didn't mention it, because I'm sure the Pre will have it in the future, just doesn't now.