Bars & Bottles: Krug Park http://www.krugpark.com/ Beer Corner USA (3 bars and a bottle shop all in one) http://beercornerusa.com/ Many Hy-Vee Groceries have good bottle selections. I really like the Hy-Vee at 14591 Stony Brook Boulevard Brew Pubs: Upstream Brewing http://www.upstreambrewing.com/ Nebraska Brewing Company http://nebraskabrewingco.com/main.asp Brewery Tours: Lucky Bucket http://www.luckybucketbrewing.com/ Specialty: Like Arcades? if so, visit Beercade http://www.thebeercade.com/ Like Single Malt Scotch? http://www.dundeedell.com/single malt.html What are you looking to do? Also, note that from Omaha to Iowa is a short drive so there may be bottles there you would like to try. Founders (no special releases), Bell's, and I'm sure there are others.
TomClem nailed it pretty much on the head though I would also throw in Jake's, which is in Benson and is across the street from Krug Park. If you are out west, Brix also has a decent bottle selection and Lauter Tun is a good beer bar. If you want a great Belgian/French meal with a great selection of Belgians, Dario's is the place. And if you want a dive beer bar with cheap beer, Brass Monkey is always a good time.
I would stay in Old Market and do the following: Start at Slowdown for happy hour 4 to 7 1/2 priced beers usually have a good selection of local and always have Odell's, Goose Island, Rogue Next: Go to The Boiler Room and have house cured meat plate and one of the best Manhattan's you will ever taste. Finally: 801 Chophouse: Sit in a booth in the bar watch a ball game and order the Maytag Blue Cheese Potato Chips a Garbage Salad and the Double Bone Pork Chop this dish is a religious experience. PS: Not a cheap evening, but you wont be disappointed
These are great suggestions though not really beer focused. The Boiler Room is amazing (as is the similar Grey Plume--both chefs are james beard nominees), but saying it wont be cheap is an understatement
Another small specialty shop is Moonstruck Meadery. http://moonstruckmead.com/ Check their facebook if you plan to attend as they have closed a time or two due to being sold out of mead.
If you're staying in a hotel downtown... start at The Library Pub ---> Krug Park --->Jake's Cigars & Spirits ---> Crescent Moon/Max's n Joe's/Huber Haus ---> The Upstream ---> Hotel. But that's just me.
