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If env ruby is Ruby 2.0 or 1.9, try either: Editing PATH or TM_RUBY in Preferences > Variables. Changing #!/usr/bin/env ruby to #!/usr/bin/ruby Source > Menu Actions > Comments > Comment Line / Selection. Or try temporarily deleting bundles. From [TxMt] TM2 error running Comment Line/Selection - Google Groups: Your bundles are likely messed up. ...
Supertab triggers insert-mode completion only when there is non-whitespace text before the cursor. Behind whitespace, or at the beginning of a line, a <Tab> character should be inserted. Something's wrong with your setup. Note that you can always insert a literal <Tab> with <C-v><Tab> (on Windows, you may have to use <C-q>).
Keep the plugins under git repositories. For your particular needs I think you could make a repository and use branches and git submodules (most of the plugins are under git anyways, so you can keep them up to date or use different versions even). A downside is that you can't use the Package Control, but you can use github to sync the setting across machines ...
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