A text book I'm using for grammar example sentences has this:

飛行機で三時間は掛かりますよ。
It will take at least three hours by plane.

The key point is は but it doesn't say if this is [ha] or [wa]. I would guess [wa] because it looks more like a particle.

You're right, it's the particle [wa]. I would say it's more emphasizing that it IS three hours, vs. literally meaning *at least*, but you seem to have figured that out as well!

Also, there wouldn't be a random 'ha' in between words...

Yes, the reading is "wa". "ga" wouldn't actually make sense here
since it's not the "3 hour trip" that is being emphasized, but rather
the fact that it will take "at least 3 hours", which is expressed by
the verb.

Although the sentence literally means "the trip will take 3 hours", it's
really saying "the trip will take 3 hours and can't be completed in less
time than that". So, in the end, it's about the same as saying "it'll take
at least 3 hours".

Btw, when you need to put emphasis on the verb, you'll generally use "wa".
"Ga" places heavy emphasis on the subject that directly precedes it.

Read the "wa" vs. "ga" article in Making Sense of Japanese by Jay Rubin.
It'll clear everything up.

Thanks for those replies.

I have a copy of Making Sense of Japanese. I read it when I bought it, but that was when I just starting with Japanese. When you started talking about emphasizing things before/after the particle it did sound familiar. I'll dig that book out for another read now I'm not an absolute beginner!!