• I did a big David Allen (GTD) style brain-dump (into OmniOutliner) and created an organized Project List in OmniOutliner
• I then move those projects and related reference material into my own Confluence server. The global access makes up for the extra clicks (hence transfer from capture in OO to Confluence)
• I’ve moved completely to Subversion for checked in code. Everything gets checked in (svn+ssh and SSH keys makes things work well)
• I use JIRA for task/effort tracking (I wrote a GreaseMonkey script to assist in automatically tracking time spent)

At some point (on the todo list) I’ll create a better integrated task system as there’s still a bit of friction between what I put in my OO Action List and what I put in JIRA.