Wow, I have the same issue - sometimes the subl command either opens an empty window or opens ane existing window with another project I'm working on.

Anyway, here are some methods to open a project folder up in sublime text. All tested on OSX, but I imagine the menu names are the same in Linux and Windows.

1. Go to 'File' > 'Open', select the folder with your project, and click 'Open' (CMD+o on a mac).
2. Drag and drop the folder on to the sublime text application in your dock or windows bar.

Also, you can add multiple folders from anywhere to one project by navigating to 'Project' > 'Add Folder To Project', then go to 'Project' > 'Save Project As' to create a quick shortcut.

To get the sub l. command to work:

1) Check this SublimeText2 info out first:

http://www.sublimetext.com/docs/2/osx_command_line.html

2) That didn't work for me, so I looked further.

Found this easy answer (for Macs) on Stackoverflow:

First, check to see if your Sublime Text2 is in your Applications folder. (If not, move it there.)

Go to your terminal and type:

open -a Finder /usr/bin

This will open your Finder to the /usr/bin directory. Once you're there open a new Finder window (you can click on the finder icon in your tray), go to Applications, right click on the Sublime Text icon and go to Show Package Contents folder, then to Contents folder, SharedSupport folder, then bin folder. Copy the subl file and paste it into the other Finder window showing /usr/bin

That's it! You should be set to use the command:

subl .