My local shop is Just Trains in Concord CA. It's an excellent shop. And there's a nice big test layout to play with. I mostly pre-order stuff.
Down in Santa Clara CA (right near San Jose) is The Train Shop, another excellent store. I used to go there regularly, but it's a 45 minute drive. Just Trains is about 20 minutes.
Franciscan Hobbies in San Francisco used to be fun, but it went radically downhill when Bill Gunther died.
Berkeley Hardware in Berkeley CA has its moments. Right now, parking is difficult, so I tend not to drop by. They used to have their own parking lot. Not a GREAT store, but: "has its moments".
Because of my local shop(s), I don't do much mail order. I've used Trainworld, and like them. For DCC stuff, I usually use Litchfield, rather than go through my shop. Brass, I've ordered through my local shop.
Ed
My go-to outlet is Model Train Stuff (MB Klein). Unfortunately, they do not do pre-ordering (a long time ago, they actually did). For pre-ordering, I like Tony's Train Exchange in Vermont (tonystrains.com). Their prices beat most of their competitors. E.g., for the upcoming BLI ATSF class 4000 Mikado, the list price is $500. Most dealers charge $400 or more. Tonystrains price is $370.
For brass, brasstrains.com is the go-to store; they have by far the biggest collection and the most used merchandise. Especially for pre-orders, another reliable and often well-priced source is BPL Brassworks.
https://tstage9.wixsite.com/nyc-modeling
Time...It marches on...without ever turning around to see if anyone is even keeping in step.
My old LHS back n Massachusetts was my favorite. He gave me very good prices on expensive stuff like locomotives, and the tiny shop was always well stocked. Unfortunately, the landlord of his little strip mall got greedy, jacked up the rent and it became time to retire. I could order stuff from Walthers through him, get any sale prices they offered, and pay no shipping.
I've also bought from Trainworld. They have great prices, often have items that are sold out everywhere else, and on at least two occasions I've ordered on Wednesday evening and had trains delivered the next day.
It takes an iron man to play with a toy iron horse.
I notice that some companys are exceding the bar as far as shipping etc. This might get locked but I will risk it. My favorites are Train World for bargins, Model Train Stuff for stuff just released, Yankee Dabler for decoders and such and just started using Linchfield Station for other DCC related stuff, real cheap shipping here so good place to go if you need 1 or 2 items. Unfortinally I can't recommend any b&b anymore, most have left my area and the remaining ones just don't cut it.