snip> My first thought was the coastal route, but if I want to see the first stage (Nevada City to Sacarmento) it looks like a better (i.e. direct) route is to Klamath, Altamont and down.
I know nothing, I've only been to OR once and that was for business in Portland 20 years ago. I've only just started looking at this and have gotten no further than trying to pull info off the 'net, which hasn't been a fruitful search. About all I know is what I can surmise from Google Maps.
First I think you should be very careful with Google Maps. It cost someone his life a couple of years ago when he got lost in the mountains west of Grants Pass and that was in a car. If you don't have a real good sense of the area, particularly away from cities, or how to use Google maps, then I don't recommend relying on it.
Second it would have helped if you gave us better idea of your thoughts south of Klamath. And are you moteling or camping? Time frame?
I think you have 4 choices:
1) Eugene to the coast, then south, then finding a route back east to Nevada City. Not an easy nor direct proposition. Probably the longest route.
2) Eugene straight south through Ashland, through Mt. Shasta and then to Nevada City.
3) Eugene to Klamath (by way of OR 58), to Weed, CA (by way of US 97) to Mt. Shasta City, then to CA 89 south to NC.
4) Eugene -> Klamath -> Alturas -> Susanville -> Lake Alamanor to last portion of choice 3.
Choice 1 is of course the best for scenery and touring facilities. The problem in my eyes is getting back from the coast to Sacto area. Once in CA on the coast, you have few choices: 36, 20 or something further south around the top of the Bay Area. It is the long way around. CA 36 is very climby with very limited services.
Choice 2 requires a lot of minor road navigation through southern OR. It also involves a lot of up and down, plus Siskiyou Pass. I've researched some of the roads but can't comment on how well it supports a touring cyclist. There are plenty of towns so a credit card moteling trip is quite doable. Once you're near Mt. Shasta City the choice is pretty clear. Either follow CA89 through the foothills, Lassen NP, and on south to Nevada City or take I5/99 through Redding and such, through the western edge of the Sacramento Valley then up to Nevada City.
Choice 3 is in my view more direct than riding through the Ashland area. Tip-off is this is the railroad's preferred route - direct and better grades. A few towns and plenty of places to camp. Once in Klamath, turning back towards Weed brings you back towards Mt. Shasta City and highway 89. CA 89 is a fine two-lane road, though it has occasional logging truck traffic and can be narrow in places. At the junction with CA 49 you could then turn west towards Nevada City.
Choice 4 heads further southeast to either Alturas or continues on CA 139. This route is pretty desolate with very few services south of Alturas for a long way. Can't speak to CA 139 as it's been 40 years since I was last on it though it appears to be more direct. Once reaching Susanville and heading west to Lake Almanor you could pick up the remainder of the choice 3 route.
Your route choice then depends a great deal on how much time you have and where you plan to stay. Good luck.
cg
edited 28 Dec 2009: You might want to look at the comments regarding CA 89 in the discussion about the Sierra Cascades Route.
