If I were to buy a TJ, the year of the model would play almost no role in my decision. Sure, there's a few considerations you'll have between some years of TJs, but they're pretty minimal. The biggest concerns would be finding one in good condition with reasonable mileage, no rust, and no stupid mods like 4" rough country lifts, car alarms, etc.
It's not like buying a JK where the 2012 and later models have a different engine. Most TJs are very similar outside of what submodel you choose (i.e. 2.4L vs 4.0 or TJ vs LJ, rubicon vs SE, etc.).
If you really get to a situation with all else being equal, the '05s and '06s have some specific issues to them, but at worst it'll cost a couple hundred dollars and minor work to fix if you are unlucky enough to encounter them.