+1 for flashlight in device menu. Always my first patch, though it can sometimes be slightly flaky.
Nokia used to have a dedicated torch button. Given how often that bright little light can be useful, I'm surprised "hold volume button for flashlight" or something similar isn't a standard option on phones.
I've never made a list of my favorite apps, but here goes!
My picks from app catalog:
Picsel Smart Office is nice for documents. It also has a better/more stable PDF browser than the stock one, though you have to start it and open the PDFs yourself.
Photo Effects Pro can sometimes be handy if you want to touch up or shrink pics.
Also, if you use DropBox, Dropboxify or Explorer for Dropbox. (Note that Dropboxify requires a small DIY fix to work properly since DB changed a URL and the developer never officially fixed it.)
drPodder (I think I have a paid version?) for podcasts. I use the **** out of this one. On wifi at home, I download the podcasts then listen over bluetooth in the car. There are more recent drPodder derivatives too, some in Preware I think.
Quell (I use Quell HD) is a nice little thinking game. Angry Birds also work well. Not a big gamer, but sometimes if you're bored on the train it's nice.
FlightView (free, I think) is super useful if you travel ever.
Homebrew Google Maps is nice.
MojoWhatsup if you use whatsapp. (I have one friend in the UK I keep in touch with using this.)
Sort of Homebrew... there's nDrive beta maps application with really nice voice nav, but you have to pay for the maps which are from 2011.
InternalzPro is handy for browsing files and editing text files when you want to tinker.
BirthdayList. I dunno where I got it, but this aggregates all the birthdays coming up. If you have a Facebook account linked, this is kind of nice since the phone knows all their birthdays but never tells you until you ask! If you see one you want to remember, there's a button to add an active reminder to your calendar.
Edit: Also, there's a way to update from webOS 2.1 to 2.2.4. I think that added the in-built Skype (can be used via the regular phone app!) when I had a Pre 2? It also updates the web browser which fixes some things and introduces a new little bug or two, as I recall. Little fuzzy on this as my Sprint FrankenPre 2 was the gateway to a Pre 3.