I started using CFEclipse a few months ago when I got FlexBuilder, it just made sense for a CF/Flex project. It was definitely an adjustment after years of using Dreamweaver and there were immediately some things I liked, but also some annoyances that I took for granted in DW. One of those annoyances was that line numbers never show up by Default for CF files...however I dug around in the preferences a bit and found that there is indeed an option to turn on line numbers permanently, so they will always show when you edit CF files.
Go to Window > Preferences > CFEclipse > Editor and check the "Show line numbers" option.
May be obvious to some, but for someone just getting into CFEclipse I was very happy to find this setting!
Tip #2 is an issue I ran into when I updated to version 1.3. I ran the updater from the "Find Updates" feature, and restarted just to be safe, but I started getting all sorts of errors when I tried to open CF files.
On a hunch I went in to Help > Software Updates > Manage Configuration, expanded the tree and noticed that 1.2 was still listed in addition to 1.3. I disabled 1.2, and the problems went away. Makes sense that having two versions running simultaneously would make Eclipse very unhappy.