First Trip to Europe: Poland > Germany > Belgium (?)

I would rethink think the Eurail pass. You can buy an inexpensive Sparpreis ticket from Berlin to Bonn. These are nonrefundable train tickets that work like airline tickets (miss your train and lose your ticket). Right now, I'm seeing prices of 43 to 59 EUR for trains, depending what time of day you want to travel on July 4.
From Bonn you are right next to Belgium. I'll wait for someone with more knowledge of the rail options there.

Do you have a chance to spend a day in Krakow. It wasn't damaged much in WWII.

Not sure about rail passes, but they seem so expensive these days. Can you rent a car?

If you are visiting Netherlands, Belgium and Luxembourg, the I suggest visiting these cities, Amsterdam, Gent, Brugges, Brussels, Luxembourg city and Viaden, Luxembourg. Wait, Viaden may not have a rail station.

Rail tickets in Belgium are relatively cheap and usually far less than the daily cost of a rail pass. Just buy the tickets at the station.

For the longer train rides in Germany, if you can commit to riding a specific train at a specific time, buy your tickets online in advanced directly from Deutsche Bahn. For any shorter trips, you can buy regional day passes that are an excellent bargain compared to anything that a ticket reseller like Eurail can offer. You can buy these at the station.

If you had several trips in Germany, then I'd consider a German Rail Pass, which also covers some trains to Brussels. But the Belgian trips are likely to be relatively shorter and cheaper, if your exploration is focused there. There's also a cheaper pass for just Benelux, but it's not a popular choice.

Thank you all for you recommendations regarding Eurail vs point tickets. We will be taking day trips out of Berlin and most likely staying in Bornheim for the conference, so we take the rail into Bonn. Thought maybe the pass would be worth it for that.

No. Bornheim to Bonn is price level 2b local ticket in the Rhein-Sieg Verkehrsverbund (aka Cologne-Bonn Transit authority). Depending on where you are staying, this may be a bus. Ticket is 3.80 EUR each way, and you can buy 4 pack of one way ticket for 14.50 EUR. You can also get a weekly commuter ticket for 31 EUR.
https://www.vrsinfo.de/englisch/the-vrs/vrs-about-us.html

You say "we". How many people?

Same situation in Berlin. Day tickets are available for the surrounding district. Your hosts in Berlin should know all of this if they've lived there longer than a couple of weeks.

"we" is one other and myself for most of the trip. For the conference, it will be 4 of us.

Spend a little time at this site to see how it works.
https://www.bahn.com/i/view/USA/en/prices/germany/regional-offers-overview.shtml

I'd start by looking at open-jaw flights (multiple destination option) and seeing what's feasible (timing, price, connections) from wherever you are in the U.S. You may have tons of options if you're flying out of New York, but pretty limited ones if it's Denver or Detroit.

At the same time, I'd use bahn.de (the German train website). It has schedules for all of Europe, and see how long it takes to get to another city. It looks like you'll have to travel to Köln for a high-speed train, but then Europe's your oyster. Paris, Brussels, Amsterdam are just a few. Once you're on the train, it really isn't a big difference if it's a 2 or 4-hour journey.

If you want to keep hotel expenses low, Belgium and Netherlands are better (Paris is expensive). You can stay in Ghent (lovely city and the cheapest) and day trip to Brussels, Bruges, even Antwerp. In the Netherlands, Amsterdam is the most expensive, but you can easily day trip there while staying a smaller, yet interesting, city, maybe Haarlem. The trains are fast and frequent, making it pretty easy to visit Utrecht, The Hague, Rotterdam . . . .

Berlin has so many things to see. Why would you want to spend your time there day-tripping to other places?

Before you think of buying a rail pass, read this from The Man In Seat 61 and make sure you understand all his points: http://tinyurl.com/bkw4u6c

If you want to know the real price of inexpensive advance tickets, here's his list of where to buy them: http://tinyurl.com/bo8x6o6

Thank you for the recommendations to get more familiar with travel options, it is extremely helpful!