Via Alpina, 3100mi (4989km), is Europe’s best trans-Alps trail.
In the summer of 2005 signage was completed for the entire route. Start packing.
Hikers choose from 5 main colour coded routes. The Red Trail, for example, crosses borders 44 times and traverses the Alps in 161 distinct stages.
The Via Alpina includes some of the most famous hikes in the alps: the Tour du Mont Blanc in France, the Triglav Lakes Valley Circuit in Slovenia, and the Col du Grand-Saint-Bernard between Switzerland and Italy, among them.
The official website is excellent offering detailed information on trail stages, hiking distances, GPS coordinates, challenge levels, and lodging options from huts (or refuges, in Alpine parlance) to chalets. In 5 languages!
NEED TO KNOW: In June and September there’s usually ample space in the hut systems along the Via Alpina. In July and August—or if you’re traveling with a large group—it’s smart to plan ahead. The Via Alpina Web site (www.via-alpina.org) lists contact information for huts, lodges, chalets, and B&Bs along each stage of the trail.
Another good starting point is Alps Travel along the Via Alpina – National Geographic Adventure Magazine
besthike.com 
My wife and I just finished hiking the Via Alpina in 2009 over 111 days across 8 countries. Great time, 700,000 feet of ascents and descents, but lots of weather challenges. Check out my website for photos and info. My book chronicling our journey, Over the Top & Back Again (published fall 2010), tells the real story. Also, Backpacking Light mag just ran a feature article w/photos about our trek.