You can try DeepMiner. It is good for scrapping, rank position, generating long tails and keyword suggestions. You can export the data to document for later analytics. You can find popular keywords that people are searching for. 7 major engines are supported, Google, Yahoo, AOL, Amazon, YouTube, Ask, Bing. It supports multi-threading so it is very very fast scrapper. BTW you must use proxy list if you plan to scrap thousands and thousands of keywords.
Using the good ol' free Google Keyword Planner is great. But there is an alternate universe of Long Tail keyword phrases that live in Google's other database--namely, their "Autocomplete database." That's the database that is accessed when you're typing queries into the Google search box (notice that list of suggested keywords that pop up as you type?)
The limit on manual keywords could be higher. I personally wish we could input 10,000 keywords at a time, instead of 200. However, I understand the costs that Long Tail Pro has to maintain each time a new manual keyword is input. Not a deal breaker, I just wish the limit was higher. (To be fair, I don't think most keyword tools have a bulk manual option at all).