Well,
If your ONLINE backup is not flushign the log files (please see http://blogs.msdn.com/exchange/archive/2004/06/21/161564.aspx for more on Exchange backups) - there is something wrong. That should be addressed first. There must be something either in the backup log file or the application log file when backup does not flush the log files. Again, this should happen with online backups.
Now, if you are already in the situation where there are too many log files, the disk is full and you need to remove some log files manually to be able to start, please see the following articles (depending on the Exchange version you use):
240145 XADM: How to Tell Which Transaction Log Files Can Be Safely Removed
http://support.microsoft.com/?id=240145
182961 XADM: Using Eseutil to Determine Which Logs Have Been Committed
http://support.microsoft.com/?id=182961