I have the paper work for obtaining a B visa, but I have heard stroes that Penang only offers 90 day visas. Any truth to that? Would Singapore or KL be a better choice with better chance to be granted a one year B visa?

You are aware of the need for a work permit with more than 6 months or so validity to obtain a multi entry visa from most Consulates (if they issue at all)? There is a big step from single to multi at most local consulates.

Penang also have been insisting on a Letter of Acceptance issued by Labour (not just the A5 sized WP3 Receipt which given for a succesfull WP application) plus 8 million Company Capitalisation, these along with the WP plus the usual MFA list of company papers papers for a One Year Multiple Entry Non Immigrant Type 'B' Visa - see link below:

.http://www.mfa.go.th...482.php?id=2492

All the OP is asking for is the best place to get a 1 year Non-B visa and says he has all the paper work.

I would reccomend Suvannakhet Lao or Vienteine. Even if you have all the paper work from your employer you will only get a 60 or 90 day Non-B visa and then when you are back you need to go through the steps of obtaining a Work Permit with your employer and after some time back and forth to the Labor department and Immigration you will eventually get a 1 year B visa but probably not before 6 months.

According to http://www.mfa.go.th/web/2482.php?id=2492

- It is recommended that the applicant should apply for visa at the Thai Embassy/ Consulate in the country where he/she has the residence

From the OP:

I have the paper work for obtaining a B visa...

"All the paperwork" is vague, because the requirements vary depending on the purpose for which you apply for the non-B visa, and apparently also vary from one consulate to another for the same purpose of application. From memory, the multiple-entry non-B visa is available for any of the following purposes.

1. Frequent travel to Thailand as the employee of a company located outside Thailand for the purpose of conducting business in Thailand.
   
2. Travel to Thailand for the purpose of obtaining a work permit and taking up employment with a Thai company.
   
3. Travel to Thailand for the purpose of working in a Thai company for which the visa applicant already has a work permit but does not qualify for extensions of stay for the reason of employment.