What are the possible upgrades to a 95' Cannondale M900?
I had a similar era KHS Alite3000 - Most moving parts had been replaced from wear over its life, but pretty much original. AT 10.5kg, RockShox Judy's, XT components etc, it is a light, fast and agile bike. Like you, I gave up serious riding for kids, got back into it last year. The KHS, despite my fondness for the bike, has been given away in favor of a new bike. Like cars, bikes have moved a long way in 20 years, and the "practical" option is to replace it - especially if you ride off road.  

The main reasons for me to replace rather than upgrade were cost exceeding the total cost of a new bike, no disk mounts and the old frame geometry not suitable for modern forks- back then 50mm was considered long travel, now 120 typical for XC. 

If you really want to upgrade it, cheapest bet would probably be a "donor" bike. Getting decent forks with V brake bosses is next to impossible, so disks on the front would be easiest. Unless you got some second hand quality forks with V brake bosses. 

What I would do is tune it up, replace any obviously worn out bits, and buy my son a new or 2-3 year old secondhand bike.