What dictionaries (online, software-based or in paper form) explain the origins of a word and its evolution over time? E.g. how the character was once written, how the usage – and the meaning – changed over time.
Wen Lin is an amazing piece of software that has all of the etymological features you are looking for. The central downside is that it is a bit pricey. Most universities have a copy, though, and there may be the opportunity to get some kind of student pricing discount. (Not sure if that applies to your case.)
zhongwen.com has a very limited amount of information on each character's origin.
This is an excellent one (and it's free too ;) )
In this post I gave an overview of online resources:
On http://ctext.org/dictionary.pl?if=en you can see how a character evolved, the simplified and traditional characters.
Another similar website is http://www.chineseetymology.org/CharacterEtymology.aspx .
Zdict is completely in Chinese: http://www.zdic.net/zd/zi/ZdicE7Zdic9BZdicAE.htm
Here is another website in Chinese (that only supports transitional characters): http://alphads10-2.hkbu.edu.hk/~lcprichi/
As Aristide mentioned http://www.yellowbridge.com has similar functionality.
Although it doesn't show how the characters evolved, I also like http://zhongwen.com It explains how characters are composed out of other characters.
In terms of the individual 漢字 (characters), there's the classic 說文解字 (Shuowen Jiezi) written in the 1st to 2nd century AD, which is the first and the most authoritative Chinese dictionary to attempt to trace the origin and evolution of each character. An online version is available here, or ZDict as mentioned above also contains the Shuowen entry.
The obvious drawback is that you need to know how to read 文言文 (classical Chinese). Be aware also that, although traditionally considered the gold standard for Chinese etymology, recent archaeological findings have necessitated new derivations for some characters; the Wikipedia page has a general explanation on this.
There's a list of etymology resources (including a couple already mentioned) on this page: http://mandarinportal.com/etymology.php
I like http://chinese-characters.org It's simple and clear.
https://www.kickstarter.com/projects/johnrenfroe/outlier-dictionary-of-chinese-characters this project on Kickstartes sound interesting.
Here's some sites I've looked up for you. Sorry if these are not what you are looking for.