Well, for those of you who care about your bikes getting muddy but want to stay in shape I have some suggestions that are working for me just as if I was riding my mountain bike every day:
1) Practice Yoga regularly: I try to get at least 3 or 4 yoga classes per week. In particular I think Vinyasa or Power Yoga combined with Bikram Yoga is a great combination to keep your core muscles in check. Plus I get my fix of warm weather with those type of Yoga practice where the room is kept at a warm temperature. With my Yoga practice, I have also developed my upper body (arms, shoulders, back) which I find it quite important for biking. Having a upper strong body facilitates bike handling, in particular the very heavy downhill bikes. Plus it keeps those extra pounds under control, in particular during the winter season.
2) Go to Tahoe and ski: I try to go to Tahoe one day a week. Yep, it is a long day driving both ways the same day, but it is not that bad if you get a friend to come with you. I recommend Sugar Bowl which is one of the closest ski areas to the Bay Area, right off the 80 hwy. Mountain biking and skiing have so many similarities! and you can be all day long outdoors without getting muddy or wet. This is me in Tahoe last summer flying with my DH bike:
And this is me in Tahoe this winter flying with my DH skis:
3) Get a single speed bike: I decided to make my hardtail gear bike into a single speed. I equipped it with fenders and take it everywhere. Since the bike has no gears and no suspension, then it has way less components and parts that get damaged with the mud. Plus this bike is helping me to build some more leg power. I know it is hard to do some of the very steep climbs in a single speed, but I just get ready to get off my bike and run up the hill to keep up with my friends riding geared bikes.
4) Danny Forer's bike and rain guide: Read the guide my friend wrote with many awesome tips to stay warm and dry during long rides under the rain. Click on this link.
5) Stay away from the muddy trails: Riding trails when they are muddy actually is not that good for the trails. So if I can avoid it, I don't ride bikes on muddy trails. I suggest riding the fire roads in Mt. Tam (Old Rail Road, Elderidge, etc..) or the fire roads in the Headlands (Coastal, Miwok). Although I do understand that fire road riding is quite boring.