Hermes thus far. It took a few tries to get it to work, but its pretty awesome to have someone call and their picture shows up. Or what-ever picture they had on Facebook. Since I usually check facebook once a day or so, I've already associated everyone with their latest picture/avatar/icon
Also, some people complain about the email. But pulling from my own IMAP server, it just freakin' rocks. I've got all my folders, it updates with new mail right on time. And thus far its been rock solid.
eCoach is good, enjoying it with my Zephyr HXM heart rate monitor (although its nothing compared to run.gps for WinMo, then of course you have to figure in that run-gps costs money).
I thought bounce was pretty wow, but otherwise agree nothing stands out massively.
Min is Petrovich a application that Qwerty12 developed that allows you to send files via Bluetooth/email ect. An application that should have been intergrated into the phone from the start. Please test and vote to get it into mainstream. I have been using it for a while and it is so simple and easy to use but serves a great purpose.
Also Rdesktop and ssh client have worked flawlessly.
Outside of that I would have to choose the combined magic of gPodder and the FM transmitter. It's perfect for my long commutes for listening to audiobooks and other podcasts. Back with my n95, I had to do all this stuff manually (downloading to and transferring to the phone). Where as now, gPodder does all that work and the FM transmitter lets me slide the n900 into the visor near the antenna to listen over the stereo instead of having to hold (like the n95) the phone up to my ear to hear it while I drive.
Pidgin is probably more important to me but my n95 already had nimbuzz and another program. So the gpodder and the fmtransmitter have been more of a big upgrade for me.
Aside from Phone/Calendar/Contacts/E-Mail/MicroB (which are obvious), I'd say Xournal is my favorite app so far. While I've only used it a few times on my n900, I use fairly regularly on my desktop and expect it'll start getting more use on my phone.
Once I figure out a solution for two-way syncing between Conboy (n900) and Tomboy (desktop), Conboy will probably be up there as well.
