thegildedgopher, I put a Recon Silver on a '03 Gary Fisher 3+ which originally had a RS "U-Turn" fork that was adjustable (on the fly) from 80 to 110mm. I put a 130 mm Recon on it. The resulting change in geometry was great. More playful, more aggressive, especially going down. Definitely changed the bike from an XC feel to more of a trail feel. I know comparing the Sugar and Marlin isn't apples to apples, but sometimes the change in geo by increasing fork travel isn't a bad thing. As for the Recon Silver... it's really a decent air fork. Supports disk and rim brakes. Does surprisingly well on subtle chatter, and more than capable of decent hard hits. Keep in mind, though, 130mm vs the 100 you're considering.
I remember the Marlin. Used to see them all over the place. Honestly, I think it'd be cool to rake it back a little with a longer fork. If it were me, I'd try a 110mm on it. But I'm far more a trail bike guy than an XC bike guy. As for investing in and worrying about parts for the Marlin, don't. Although my Sugar is a couple years newer, it's built on the same standards as your Marlin. Every part I need is still available, even the proprietary suspension bushings, which Trek still has in stock to this day.