We have used a few tools earlier. We now use a GitHub private repository to maintain various developer TBD lists (as .md files) and issue tracking because of the following advantages:
- Developers are already using GitHub and they don't need to learn anything new.
- Developers can use whatever tool they are comfortable with to maintain TBD list; command line or graphical editors, GitHub web interface or plenty of mobile clients
- Markdown support
- Reliable backup
- Merging and revision history
- Flexible file organization for different projects and modules
