With the deployment of 1.29.0-wmf.5 which just finished on all wikis, several changes were made in user interface colors.
* Gray boxes (TOC, Wikitables, catlinks, thumbnails, elements in history etc.) has changed from #f9f9f9 as background to #f8f9fa and #aaa as border to #a2a9b1. [1] This change is almost not noticeable but in order to keep consistency between all elements of a wiki page, change such usages in your Mediawiki:Common.css (for example for infoboxes).
* Search results border and background colors also changed and this one is also not noticeable. [2]
* "You have new message in your talk page" notification color has changed from #f9c557 to #fc3 (yellow). [3] This change is noticeable.

These all are parts of works ongoing by WMF designers and engineers to have a standard UI [4] using standard colors picked from Wikimedia color palette. [5]

Using consistent colors helps users have better experience and strengthen branding. Also these colors have passed WCAG standard for accessibility (for color blind people). Lots have been done already. Such as content translation [6] wikipedia.org portal [7] [8], mobile frontend [9], Echo email notification [10], Deffered changes [11] ORES review tool [12], disambig icon [13] [14], WMF wiki main page [15] and a lot more.

So I recommend you to use the color palette [5] as much as possible.

I must explicitly note that I did a little and I don't think I can talk on behalf of UI-standardization team :)

[1]: https://gerrit.wikimedia.org/r/324534
[2]: https://gerrit.wikimedia.org/r/324549
[3]: https://gerrit.wikimedia.org/r/324161
[4]: https://phabricator.wikimedia.org/tag/ui-standardization
[5]: Wikimedia color palette: https://phabricator.wikimedia.org/M82
[6]: https://gerrit.wikimedia.org/r/321609
[7]: https://gerrit.wikimedia.org/r/322831
[8]: https://gerrit.wikimedia.org/r/325057
[9]: https://gerrit.wikimedia.org/r/317746
[10]: https://gerrit.wikimedia.org/r/323554
[11]: https://gerrit.wikimedia.org/r/323558
[12]: https://gerrit.wikimedia.org/r/320341
[13]: https://commons.wikimedia.org/wiki/File:Disambig.svg
[14]: https://commons.wikimedia.org/wiki/File:Disambig_gray.svg
[15]: https://wikimediafoundation.org/wiki/Home