would prefer

Analysing subjunctives is not my greatest strength, so I HOPE that the following explanation is roughly correct! 

(I edited just after posting to correct a typo)

Tuongvan

Can I use WOULD PREFER the same way?i.e.Can I say" I would prefer he went to meet Mr Brown now." instead?

"I would prefer he..." is not a form of words that comes very naturally to me (I would usually say "I would prefer it if he went to meet Mr Brown now.") -- but others may differ. If you do use "I would prefer he...", then strictly speaking I think it should be "I would prefer he go to meet Mr Brown" (this is the subjunctive, see below). The problem is that this sounds rather old-fashioned and stilted (to me), and I'm guessing that this perceived awkwardness influences some people to write "I would prefer he went" instead.

Tuongvan

b/The Pentagon said it would prefer that the withdrawal plan and the education benefits not be considered with the war funding.
Why don't they say'it would prefer that the withdrawal plan and the education benefits would not be considered /were not considered with the war funding.'?

"not be considered" is the subjunctive form, which, to quote from Wikipedia, is "a verb mood that ... is typically used in dependent clauses to express wishes, commands, emotion, possibility, judgment, necessity, or statements that are contrary to fact at present." "Prefer" is one of the verbs that it is used with. Your example with "would not be considered" is unnatural. "were not considered" seems more plausible, and, to be honest, I'm not sure if it's technically correct or not. But anyway, with that form of words I think I would say "would prefer it if the withdrawal plan and the education benefits were not considered with the war funding".

Tuongvan

b/He would prefer she stop calling him "Pacman"
Why don't they say'He would prefer she stopped calling him "Pacman"?

Same reason as above: subjunctive.