Ask a judge to shuffle. Neither player can cut or shuffle after a judge's shuffle, though. Also, if you cut your opponent's deck in more parts than half (3 stacks or more), it is considered a shuffle, and they have the right to cut their own deck (in halves).
I like to distribute basics, energies, and trainer cards evenly throughout my deck, and then shuffle thoroughly. I normally do this before critical matches (elimination rounds) or if I end up with no basic multiple times (means the cards are all clumped together and not truly random). It is legal to do because your cards are still randomized sufficiently afterwards and you aren't gaining an unfair advantage. Great for preventing bad starts, but it takes time to do (best to do it before the next pairings are announced, if possible).
