I'd like to start off by saying I've tried this list before, but it never really took off and I missed some things. So now I'm back.
The ponit of thi spsot is to look at the similarities between the Baratie and the Arlong arc, compared to the Water 7 and Enies Lobby arc. If you don't have an idea of who exactly wins at the end and how they do it, read 20 chapters of manga(from where the Anime ended) and come back.
I'll start by posting basic differences and get more complicated as it goes on.
1: The newly joined female character(a couple arcs or so is new) runs away(theya re the latest member as well) and ends up on another island in the hands of a powerful enemy.
2: Both interconnected arcs started out as very happy arcs. THen partway through it gets a darker storyline to it, and the next following "rescue" arc is aways pretty much a darker story and the whole thing is a bit more serious.
3: Both times the straw hats didn't have The Going Merry for some reason(or rather whatever their ship was, both times it was The Merry) and had to take another form of transportation.
4: There was a crash landing on their new form of transport each time.
5: Both times the ship was later recovered.
6: Each crew member has their own fight, but they swithc a couple of times.
7: Luffy of course faces off with "the boss" and almost loses. He then manages to do something to the enemy(he really messed up Lucci, and destroyed Arlong's maps Nami was forced to make for him) that gave him a slight boost, and finally finished them off with a pwoerful move.
8: The enemy base was destroyed both times, though not all of them damage on Enies Lobby was the Straw Hats, much of it was the Buster Call.
9: In each, the crew gets bountys after. More specifically, Luffy got a bonty starting with a 3 followed by all zeroes, but it's either a 3 or a 30 at the beginning, either way you look at it.
10: One crew member didn't really quite join but adventures with them anyways(Sanji just barely joined at the last second, Franky came along too)
11: In both, the crew member's(the kidnapped one, or the one who ran away) cried and shortly thereafter the fight began.
12: There was a major resolution at the end of each, a whole chapter or two devoted to the party and then Enies Lobby's resolution on Water 7 was pretty much a long one, if not the longest.
13: A ship gets wrecked each time. Sanji's small boat and the Going Merry both took and showed large amounts of damage.
14: There were guests along with them, Johnny and YOsaku, and then the Franky Family.
15: The giants that were gatekeepers might be comparable to the townpeople of cocoyashi, in that they started out a bit hostile and then became allies and friends.
16: Zoro loses a sword or swords and picks up a new one one that isn't his and isn't nearly as good. Both times the swords were completely destroyed.
That's 16, I'm going to bed soon. yawn discuss if you want, or try to make mroe and I'll add them.