Im not even going to get into the nonsense about HP. What a joke. LOL
Anyway, the Bay Area is home to 50 of the 500 most valuable US companies according to the Financial Times(UK) 500, 2011
That's 1 in 10 companies.
Not bad considering the Bay Area is home to only 2% of the nation's population.
Natl rank, Company, Market Capitalization 2011
2 Apple $321.0 Billion
3 Chevron $215.7 Billion
12 Oracle $169.8 Billion
13 Wells Fargo $167.4 Billion
17 Google $147.199 Billion
23 Intel $110.7 Billion
27 Cisco Systems $94.8 Billion
29 Hewlett Packard $88.6 Billion
72 eBay $40.2 Billion
82 Visa $36.4 Billion
89 Gilead Sciences $33.6 Billion
112 Franklin Resources $27.9 Billion
140 Juniper Networks $22.5 Billion
142 Yahoo $21.8 Billion
143 Charles Schwab $21.7 Billion
151 Applied Materials $20.6 Billion
154 McKesson $20.0 Billion
172 Salesforce.com $17.7 Billion
180 PG&E $17.5 Billion
187 Adobe Systems $16.7 Billion
194 Intuit $16.0 Billion
201 Agilent Technologies $15.4 Billion
219 Altera $14.1 Billion
220 Symantec $14.1 Billion
237 Gap $13.2 Billion
241 Intuitive Surgical $13.0 Billion
249 Netflix $12.5 Billion
289 Nvidia $10.9 Billion
290 Sandisk $10.9 Billion
297 Check Point Software Technologies $10.6 Billion
321 Marvell Technology $9.8 Billion
326 vMWare $9.6 Billion
327 Clorox $9.6 Billion
345 Prologis $9.1 Billion
369 Xilinx $8.5 Billion
377 Ross Stores $8.3 Billion
388 Varian Medical Systems $8.1 Billion
394 KLA Tencor $7.9 Billion
399 Linear Technology $7.6 Billion
400 Avago Technologies $7.6 Billion
404 Maxim Integrated Products $7.5 Billion
411 NXP Semiconductors $7.5 Billion
438 Lam Research $7.0 Billion
453 Electronic Arts $6.5 Billion
454 Seagate Technology $6.525 Billion
469 Atmel $6.2 Billion
471 Trimble Navigation $6.1 Billion
474 AMB Property $6.0 Billion
487 Advanced Micro Devices $5.9 Billion
496 Rovi $5.7 Billion
FT.com / UK - US 500 2011
Skimming through the list, Houston has quite a few as well. Boston too but I dont think as many as the Bay Area and Houston.
The OP might not be too far off in asking about these 3 regions since they appear to be home to about 100 of 500 the most valuable US companies.