Once I have a list of phrases, rankings, and volumes from these tools, I'll look to internal tools (maybe Excel, Access, or another database) to organize, classify, and forecast opportunity. This is where I'll estimate a competitor's traffic based on volume & position CTR, set goals for a target position, and estimate traffic based off that position's CTR and keyword volume.
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?)

Here is the part of this post that we’ve all been waiting for. How to make Long Tail Pro pay for itself! I can tell you with absolute certainty that all of this isn’t just fluff designed to try to get you to buy the product. I’ve actually done all 4 of these things – and I continue to do the top 3 to this day! This stuff really works and I make WAY more than enough money, as a result of using Long Tail Pro, to pay for itself.
3) Google: This is pretty straight forward but it’s the main reason I like it. I search for my main seed keyword in Google, and use the keywords that Google itself highlights in bold on the search results, plus the “Searches related to” section at the bottom to get keyword variations or LSI. That’s basically what Google is telling you that topic is about. No need for a thousands other tools. I use these to optimize the on page of my target pages as well.
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).