Hey Joe T - glad you took the plunge - if anything, I think this helps you get your eye in, so to speak, for figuring out which sorts of apps you like, and even some individual ones which will cross over to the Apps Store.
On your questions, a few quick thoughts:
1. Most things that are really good and 'mainstream-ish' will make it into the default repositories fairly quickly. Having said that, some good ones and more specialist ones, dont. Here's a couple I think are useful:
EIC member x99x's Fight Club - has some neat fixes, good themes and wallapers, and miscellaneous. See
this thread for better description and source URL.
Big Boss - great number of fixes and some superb utilities - BossTool is a must for recouping space to install apps to etc. - source URL is:
http://sleepers.net/iphonerepo
Add both his standard and 'Beta Experimental' sources
There are quite a few others that are worth looking at to - trying to keep this not too long for now.
2. What error do you get? May just be connectivty / server issues at times.
3. Very subjective this of course, but a few very cool and popular ones:
Touchpad - use the iPhone as an extended touchpad for your PC - requires the VNSea app to work
VNSea - pretty good native VNC client app
Books - ebook reader
Xlaunch - good launcher app for when the apps and webclips start piling up
weDict - dictionary and encyclopedia framework app - there are a number of good reference tomes to add to this available in Installer
Summerboard and Customize - the two you will have heard of that let you theme and personalize your phone
SyncJe - wireless Google Calendar (and others) sync
MobileFinder
Vnotes - voice recording app
Search - search contacts and calendar
Lots of good games - almost whatever sort of game you like by now - from Chess and Pool to Labyrinth and iPhysics and 3D games
ShowTime - basic video recording app
Pianist, Drummer, Pocket Guitar - for your iPhone band forming needs
And lots of others - browse the categories
4. Screenshot is one that many folks in here have had severe troubles with. Its a screen capture app of course. The only GUI-based one. I like this app and have used it through several firmwares now, but would admit it is badly behaved if left running in the background, especially during a respring, and can cause severe headaches. If you use it, shut it down immediately after use.
5. I don't usually blow my own site's trumpet a whole bunch in here, but I think we focus on and cover iPhone apps pretty well, including some decent length reviews, like
this one of a Voice Dialing app for instance.
6. Like on a PC, think this may vary a bit by application, in terms of where they store data and such.
Hope that is a little help ...