The fully-diluted share count for valuation purposes is ~63M.
Here's the arithmetic: According to the 2008 10K report (page 42), as of 2/13/09 there were 62.1M fully-diluted shares, including 5.5M options with an average exercise price of $8.49. Adding in the 2.5M shares issued to GSK as part of the IDX899 license gives 64.6M fully-diluted shares as of today.
However, about one third of the 5.5M options outstanding have an exercise price above the level at which the stock can realistically be expected to trade during the next few years. After excluding such options, the fully-diluted share count is approximately 63M; this is the figure I use for valuation purposes.