Time is a one-dimensional thing. A timestamp plus timezone is two-dimensional, describing a point in time, and a location. Couch views are one-dimensional (but not the GeoCouch plugin), so storing in a common zone (UTC) is wise.
Probably the most future-proof format is a string that naturally sorts in chronological order. Probably the most convenient such format is what JSON2 outputs:
> a = new Date();
Thu Jan 27 2011 18:40:52 GMT+0700 (ICT)
> JSON.stringify(a)
"2011-01-27T11:40:52.280Z"
与恶龙缠斗过久,自身亦成为恶龙;凝视深渊过久,深渊将回以凝视…