I have tried many methods for learning characters, to be honest the best one I've found is really to just write them out several times each by hand and then review them using an SRS (spaced repetition system) program.

Although the website provides SRS in the flash cards, I don't have an apple device to use the apps, so I instead use Anki (on my phone that is). Anki is an SRS flashcard system that you can create your own flash cards. I tend to comb lessons, then build a flashcard deck in Anki to review. I write the word out 10-15 times depending on complexity, and learn it in the context of a sentence from a Popup Chinese lesson or the Popup Chinese test. I put English on the 'front' and then as I review I draw the character in my head and also speak it out loud (hopefully with the appropriate tones, but my tones are trash). Once I 'flip' the card I can tell the software how well I did, didn't remember, it was easy, very easy etc. Based on my answer it'll schedule a review X days out. Also, on the back side I put the full sentence so I can read it in context and practice using it a bit each time.

There are several other methods I explored, like learning all the radicals and then creating stories for the characters. This was helpful to a point, but it started to be harder to remember the stories than it was to just remember what the character looked like.

One other thing I've found helpful in general for Chinese is the Chinese Breeze graded readers. http://www.cheng-tsui.com/store/products/chinese_breeze

Although the stories are admittedly incredibly boring/predictable, it is a great way to review characters in a way other than just flash cards. These were far more helpful at my lower levels of Chinese and aren't of much service today as they only go up to the 750 character limit right now.

In reality though, I think I've gotten the most practice in Chinese from two things:

-QQ: http://download.imqq.com/download.shtml - This is the international version so it is an English version. You can also get the full Chinese version which is a bit of an adventure.

-Sougou Input Method: http://pinyin.sogou.com/ (Click 立即下载）

QQ is basically the AOL Instant Messenger (or maybe MSN depending on your age) of China. You can find all sorts of people extremely willing to perform language exchange with you on it. Or just people ready and willing to speak Chinese only. It's a lot of fun and you'll learn tons of new words straight from native Chinese folks in 'slangy' or 日常说话 situations.

Listening comprehension is still my greatest downfall I think. I would love to hear ways to practice hearing the tonal differences beyond just 'listen more.' I have an extremely hard time hearing tones in any normally paced speech. I know I can hear them in slow speech because in the lower level lessons I have no issue determining tones when Echo repeats the speech, but man is it hard for me to pick them apart at speed.

One way I have found to practice this really is to just listen listen listen and learn new vocabulary and sentence. The more words you know,the more likely you can pick things up by context. You can check some other forum posts for TV recommendations. Although most Chinese TV is boring (IMO - and in several other people's by the looks) you can always get dubbed American movies.

Anyway, good luck! Hopefully your Chinese will end up better than mine.