[rs]

XP-Dev.com - (disclaimer: I develop and manage xp-dev.com). I'm using it at the moment for a couple of side projects (they're not startups, but more webapps) with others.

Bunch of features: http://xp-dev.com/features/

Having said that, if you really want something standalone - Trac http://trac.edgewall.org/ and Redmine http://www.redmine.org/ come to mind. There is always Bugzilla (http://www.bugzilla.org/) if you want to go old school.

Of course, you could always just use a spreadsheet to track it all (please don't laugh at this - I've seen it used oh-so-many-times in the past).