I swear by SoftMouse for colony management: https://www.softmouse.net/HomePage.do
It’s free, which is nice, and also cloud-based with a decent mobile website (no app yet though). There are some handy features, such as color-coding a good mechanism for genotype info. It doesn’t have much functionality when it comes to tracking the animals in downstream experiments, but you can assign each animal an ID so when I use an animal in an experiment I make a note of the ID. That way I can still trace it back in the SoftMouse software. There is a comment section where you can make notes about a given animal, cage, or litter - so I guess this could also be a good way to document how each animal is used.
SoftMouse has a pedigree/family tree feature in the paid version of the program but not the free version. Therefore I use an Excel spreadsheet to keep track of pedigree and breeding records in conjunction with SoftMouse. There’s some redundancy of info between these two programs but there have been times when that has come in handy so I’m still happy with the system I’ve worked out.