Kliflash basically uses a group of n words (e.g. 21 in "Intermediate" rank), and as soon as you get one word correct m times (e.g. twice), it drops out of the group and is replaced with another one. If you make a mistake, it simply stays in the group so you'll see it again in 21 words' time.
You don't even have to get it right twice in a row: IIRC getting it right one, then wrong sixty time, then right again is just fine and it'll drop out. Once a word has dropped out of its group, you'll never see it again until you restart that level.
Questions can be either Klingon–English or English–Klingon, and can be word entry or multiple-choice (though you can configure the question type if you only want to practise with one type of questions.)
Logflash, on the other hand, is a much more severe taskmaster. It follows the 'Flash' technique for learning language vocabulary described in this document, which was apparently developed by Dr. James Cooke Brown.
Basically, you have a "New Word" lesson of, say, 20 words and have to translate each Lojban word into English. If you get it right, it goes in the "Recognition 1" pile; if not, it goes into an "Error" pile.
At the end of that session, you have to practise each word in the "Error" pile until you have got it right six times in a row. This can be annoying if you got it right five times, then messed up on the sixth, but it really drills the words you don't know. When you've gone through all words in the "Error" pile, they'll end up in the "Dropback" pile.
Then you do the "Recognition 1" pile and have to translate Lojban–English again; right, it goes into "Recognition 2", wrong, it goes into Error, six times practise, then into the "Dropback"—right at the btotom.
The next level is "Recognition 3", for words you've recognised (i.e. translated Lojban–English) three times correctly, and you're asked to supply the Lojban word given the English. Do this right and they'll land in "Recall 1", where you'll be asked to translate English–Lojban again. Only then (after three times L–E and two times E–L) do they end up in the "Under Control" pile.
And the error words from the Dropback pile go into the "Recognition 1" pile, just like the words from the New Words lesson.
So you end up seeing each word more often, especially the ones you have problems with. It might make it harder to get through the entire pile of "cards", but I think it trains you better.
Unfortunately, Logflash is pretty much set up (e.g. in terms of screen layout) to work with the Lojban gismu list, so I don't think you could retrofit it to do Klingon. Stella suggested I write my own program, but I'm not sure whether I'll work up enough energy to do so.
Still, if wishes were horses, I'd like a pony.
On the other hand, I've made real paper flashcards for the 500 words which comprise the beginner's vocabulary required for the first level of the Klingon Language Certification Program, and I have a wooden box with different-sized compartments which is designed for learning things with flashcards, so maybe I can adapt that technique.