I'm glad that people are starting young to collect root beer bottles. I started seriously collecting about 4.5 years ago and I have 218 different brands. I grew up in Milwaukee so I know of many brands in Wisconsin. I'll try to give you a complete list:
Capital Brewery, Madison,
http://www.capital-brewery.com/
Gray's Brewing, Janesville,
http://www.graybrewing.com/
Northwoods Brewpub, Eau Claire,
http://www.northwoodsbrewpub.com/
Republican Root Beer, Ripon,
http://www.riponmainst.com/riponmainst/republican_ale_beer.htm
Viking Brewing, Dallas, WI,
http://www.vikingbrewing.com/products.htm
Appleton Brewing, Appleton, Makes Houdini, Shotz, Ya Der Hey, Schreiner's Restaurant (sold here:
http://www.fdlchowder.com/ )
Black Bear Soda, Milwaukee, Makes Caruso's Legacy Robusto Root Beer
Stevens Point Brewery, Stevens Point,
http://www.pointbeer.com/root_beer.php
Silver Creek Brewing, Cedarburg,
http://www.silvercreekbrewing.com/pub/ontap.html They don't bottle it yet, though they said they were going to
Lakefront Brewery, Milwaukee,
http://www.lakefrontbrewery.com/meetbeer.asp
Baumeister- from Kewaunee Bottling co. They also make Torpedo Juice, available at the Wisconsin Maritime Museum in Manitowoc
Joseph Huber Brewing, Monroe, Makes Berghoff and Blumers,
http://www.blumerssoda.com/
Dang That's Good and Dang That's Good Butterscotch, made be Imperial Flavors Beverages, Milwaukee. I'm pretty sure these are available at Discount Liquor 5031 W Oklahoma Ave Milwaukee
Twigs Beverage, Shawano, I'm not sure if they have started making Shawano Club Root Beer yet and if it's bottled
Title Town Brewing, Green Bay,
http://www.titletownbrewing.com/snocap/ As the website says, they are not yet bottling it.
I think that's it. I didn't mention Sprecher, because I figured you had it. I'm sure you have some of those, but hopefully there are some you don't have and you can take a trip across the state to get them. Good luck!