MySQL data type for 128 bit integers
I don't know what the best way necessarily is to store it -- but there's at least a better option than using a varchar(39) (or varchar(40) if you needed it signed) ; instead use a decimal(39,0).  From the mysql docs:


  Fixed-Point (Exact-Value) Types
  
  The DECIMAL and NUMERIC types store
  exact numeric data values. These types
  are used when it is important to
  preserve exact precision, for example
  with monetary data. In MySQL, NUMERIC
  is implemented as DECIMAL, so the
  following remarks about DECIMAL apply
  equally to NUMERIC.
  
  MySQL 5.1 stores DECIMAL values in
  binary format. Before MySQL 5.0.3,
  they were stored as strings. See
  Section 11.18, “Precision Math”.
  
  In a DECIMAL column declaration, the
  precision and scale can be (and
  usually is) specified; for example:

salary DECIMAL(5,2)

  
  In this example, 5 is the precision
  and 2 is the scale. The precision
  represents the number of significant
  digits that are stored for values, and
  the scale represents the number of
  digits that can be stored following
  the decimal point.
  
  Standard SQL requires that
  DECIMAL(5,2) be able to store any
  value with five digits and two
  decimals, so values that can be stored
  in the salary column range from
  -999.99 to 999.99.
  
  In standard SQL, the syntax DECIMAL(M)
  is equivalent to DECIMAL(M,0).
  Similarly, the syntax DECIMAL is
  equivalent to DECIMAL(M,0), where the
  implementation is permitted to decide
  the value of M. MySQL supports both of
  these variant forms of DECIMAL syntax.
  The default value of M is 10.
  
  If the scale is 0, DECIMAL values
  contain no decimal point or fractional
  part.
  
  The maximum number of digits for
  DECIMAL is 65, but the actual range
  for a given DECIMAL column can be
  constrained by the precision or scale
  for a given column. When such a column
  is assigned a value with more digits
  following the decimal point than are
  permitted by the specified scale, the
  value is converted to that scale. (The
  precise behavior is operating
  system-specific, but generally the
  effect is truncation to the
  permissible number of digits.)


It's stored packed, so it'll take up less space than the varchar (18 bytes, if I'm doing my math right), and I'd hope you'd be able to do math on it directly, but I've never tried with that large of a number to see what happens.