(Sorry for the late answer)
I've spent about 3 months over the course of a few trips (2 months on my first trip), and I had a list of places I wanted to see. Not all of them are 'attractions' or the usual, but nevertheless something as a geek that's been looking at the things going on in Silicon Valley from a far most of my life I wanted to see:
- Computer History Museum (you've already got that one though)
- HP Garage: 367 Addison Avenue, Palo Alto
- Shockley Semiconductor: 391 San Antonio Road, Mountain View (First 'Silicon' company)
- Googleplex and Android statues: 1600 Amphitheatre Parkway, Mountain View
- Apple campus and 'company store': 1 Infinite Loop
- Weird Stuff Warehouse (I've bought several CueCats from this place from my several visits)
- Fry's Sunnyvale ('first' Fry's in the US)
- Samovar Tea Lounge: A few in SF (the trendy place for startup geeks like Kevin Rose)
- TWiT Cottage (now TWiT Brick House): Petaluma
- Yoda fountain at Lucasfilm HQ: The Presidio, 1 Letterman Drive, SF
As I said, not all are 'family attractions' (eg. electronics stores), but things myself and my girlfriend were interested in seeing. I went to the Intel Museum, and although it was somewhat interesting I wouldn't recommend it if you're already going to the CHM, it's tiny and as you can expect, just a timeline of Intel's achievements.
A lot of these are also in The Geek Atlas O'Reilly book, and you might benefit from reading/listening to Microserfs to get a feel for how things were in the early '90s, including the places they went around the area (such as Fry's).