We have the Imaginarium (toys r us brand). Probably the best for the price. While all the brands are similar, they don't all connect to each other well. Avoid Ikea's track, the bridges are too short for Thomas trains.
We have various brands of train track and they all seem to do well together. I do agree about the Ikea bridges like pp said. The only Thomas track we have were hand me downs. We have Circo brand (Target), Imaginarium, and Melissa and Doug. We bought a lot of the track at yard sales and on ebay, of all places. My DH found a sweet deal 2 Christmases ago and that's how we got the bulk of our track.
We have a Kidkraft table with their track, the Circo brand track from Target, and a few Thomas track pieces that have come with sets and they all work well together.
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Re: Trains