I've been timelapsing for some time now with various bits of equipment and various camera setups and there's one thing that you're likely to come across even if you're shooting fully manual. Flickering.
Whether it be from cloud cover very quickly changing lighting conditions or tiny changes in aperture caused by an electronic lens. The good new is that there's a nice and easy fix to this in post...and whats more on a Windows PC it's free.
If you're looking for something fully intergrated you'll be looking at something pretty pricey. $250 for DEFlicker for Adobe After Effects. If you're happy to get the timelapse sorted and rendered out in a state ready to be further edited in another software then this is for you!
VirtualDub is where you'll need to start. A completely free open source piece of software for batch processing and converting of video files. One useful feature and the one that we will be needing is the ability to install 3rd party plugins. These can do all sorts of things but there's one plugin specifically called MSU Deflicker. This plugin was originally designed to deflicker old footage from film cameras but it can also be used on timelapses. Simply download VirtualDub, open the VD 'Plugins32' folder and unpack the MSU deflicker .vdf file into it. Now open VirtualDub, open your timelapse which you'll need to save as a video file (Lossless AVI rendered from After Effects is the best way to maintain quality), go to video-filters-add button and then select MSU Deflicker. Now save your video by going to: File-Save as AVI.
You don't really need to change any of the settings on the plugin but the web page devoted to the plugin has more details if you need! You can find a video tutorial for the process here(Length 2:30 approx):