There is a company OptionEase that has solutions to address this issue. There link is: http://www.optionease.com
I have not used their software but I have heard from friends that it is very good and ensures compliance with the SEC etc.
Sorry. I just saw this. There are several good platforms out there, depending on your specific needs.
E*Trade (Equity Edge Online)
Reach out to me directly if you want more details. Each has strengths and weaknesses. Some, like OPTRACK, are very inexpensive.
We have a SaaS based solution that's free for start-up companies with fewer than 25 option holders. It manages your cap table, option vesting, and has some really cool exit planning tools including waterfall analysis. If you contact me I can give you more info.