Just to get this out of the way now: this post is CRAZY long. I tried to cram as much detail into it as I could. I apologize if any of this is confusing and will happily clarify any of it!
Hi guys. Lurker here. I got into this hobby in September 2010 and my first and favorite fish, Brutus, a VT, has experienced occasional health problems over time. I'm sorry if some of this seems unnecessary, but I'm going to detail his tank history because he's been through a lot (in part due to my selfishness). LONG story follows:
In the beginning of September, right after I got him, Brutus spent about two weeks in a bowl until I learned that bowls were extremely unideal for bettas. He was promptly moved to a 6.6 gallon bookshelf aquarium from Petco with a couple of live plants, filter and a cheap heater. He loved it!
Everything was fine and dandy. I remember adding TSS, watching the water parameters every other day and doing necessary water changes. (I kept a log of these on my phone which I've since lost. I write them down now.) Then, one day I woke up to find that the aquarium somehow leaked water all over the table it was on. I had no explanation for this because I kept the door shut at night to keep out the cats. I'd read several reviews of the bookshelf aquarium "leaking" and I was kinda freaked out, so I gathered everything up and returned the aquarium to the store. I bought an Aqueon Deluxe 10 gallon kit instead.
I used the same gravel and old filter media (behind new filter media) from the 6.6 gal in hopes of preserving any potential beneficial bacteria. I remember adding another dose of TSS and I continued my log. Everything was again fine until I noticed one day that there was a chunk missing from the end of his caudal fin. I considered the possibility that maybe his fin was just snagged by the filter, so I didn't do anything immediately. The next day, I noticed that there was a big hole in the fin. This I found disturbing, because I had made sure there was nothing he could snag on. The day after that, I noticed that his tail was getting shorter.
http://www.nippyfish.net/finlossfinrot.html I read and re-read this page a lot once I noticed the problem with his fin. At first it really just seemed like the filter sucked up the end of his fin or he bit it, because there was never a black or bloody edge. However, several days after I first noticed the problem he had lost at least 1/3 of his fin and the end of one of his ventral fins. Being a n00b, I figured he had some kind of fin rot and I treated him once with Maracyn I & II to cover gram-positive and -negative bacteria.
It seemed to help. Nothing got worse and several weeks later his fins were actually growing back. (This makes me less likely to believe that fin nipping was ever the cause. I have never even seen him nip at his fins.)
Now, here's part of his medical history where I feel like an absolute idiot...
Brutus has a hole/gash/wound in his side. In all honesty I don't remember when I first noticed it. I think it was after I treated him with Maracyn for what I thought was fin rot. I would guesstimate the first time I saw it to be in late November or early December. I remember thinking he had some scales missing, possibly from bumping into the filter or something. I have no idea what in his tank could actually cause it, but the filter was a convenient scapegoat. I did not, until recently, realize that it is actually an open wound. And... it's turning into a nightmare.
Here is the earliest picture I have of it:

(He is still in his own 10 gallon in this picture btw, so this is November/December.)
What substantiated my belief that it was just missing scales is a) I didn't really know what missing scales looked like compared to open wounds (stupid, I know) and b) at one point it began to heal. Scales were growing back and it appeared to be healing quite well. It looks really nice in that picture compared to how it is now, ha. D:
I didn't do anything about the wound because I didn't realize it was one. I changed the water like normal. Then, on December 17th, I bought a spare 10 gallon tank because I discovered this forum and the tutorial on dividing tanks (which I thought was totally genius, haha). I divided the 10 gallon with plans to put Brutus and a new tank mate in it. I transferred the gravel and filter media from his 10 gal to the new one and bought a beautiful red veiltail who I named Julius. I noticed that after I transferred Brutus to this new 10 gal his side wound got worse. Here is a picture of him in the new tank:

You can see the wound doesn't have the same amount of scales covering it as in the previous picture. (Also, do his eyes look big? :\ Is this a mild case of popeye? Popeye can be a symptom of internal problems, right? Because...*)
Here is another picture taken a few minutes later:
I now believe he had and/or has columnaris. (I'll get to that soon.) I know that this can cause skin lesions and fin loss. It also responded well to the Maracyn I/II and have seen Maracyn II recommended to treat it. It is also contagious...
At the beginning of this month, I noticed that the same thing that originally happened to Brutus (fin seemingly disappearing, eaten up by some invisible force) was starting to happen to Julius. I paired them together because they both have (or, had :( ) really great fins IMHO, and because I thought that any health problems with Brutus were over. But the end of Julius's caudal fin seemed (and still seems) to be getting worse and worse every day. It's gone from long and flowing to raggedly and tattered. He also has greyish spots on him that are consistent to descriptions of columnaris that I've read.

Here you can see the greyish spots on him pretty well.
On January 2nd I decided to treat them in their 10 gal with Maracyn I & II. It had seemingly stopped any problems with Brutus's fins from progressing the very first time I used it on him, so I thought it might work again. I treated for the directed five days. For a couple of days after the treatment concluded, nothing looked any better, but nothing looked any worse either.
Then, I noticed that Julius's tail was getting shorter and shorter. Brutus appeared to be getting worse as well. I began a second treatment of Maracyn I & II this Tuesday.