Journaling filesystems (such as Ext3 or ReiserFS) are now being used by
default by most Linux distributions. No secure deletion program that
does filesystem-level calls can sanitize files on such filesystems,
because sensitive data and metadata can be written to the journal,
which cannot be readily accessed. Per-file secure deletion is better
implemented in the operating system.
Encrypting a whole partition with cryptoloop, for example, does not
help very much either, since there is a single key for all the parti‐
tion.
Therefore wipe is best used to sanitize a harddisk before giving it to
untrusted parties (i.e. sending your laptop for repair, or selling your
disk). Wiping size issues have been hopefully fixed (I apologize for
the long delay).