I love Asepsis. Those .DS_store files really bug me. Because I have to show hidden files to see Eclipse's .project and .classpath files, that means I also have to see the zillion .DS_store files.
Stupid, stupid file name choices by Eclipse.
(Period prefixes are default hidden on Unix, for all you Windows users.)
PS- TotalFinder is great too. Big improvement.
PPS- Tried TotalTerminal for a while. It's okay. iTerm2 is enough better that I switched.
It has a feature called "The Asepsis feature" which will redirect .DS_Store files to /usr/local/.dscache. Quite handy.