At this point I guess the only 2 ways remaining open for a short time are Messages & Alerts and Custom Links, where you still can inject JS into standard Aloha Salesforce pages. Alternatively you could try to use a community, where you can inject JS via Header and Footer.
But even these will be shutdown with Spring'16 as announced by Salesforce via Email and Knowledgebase Articles as I've described here: End of Sidebar workarounds via Messages & Alerts and Custom Links finally in Winter or Spring '16?
Moving the JS injection to Messages & Alerts is pretty easy. You can do this in less than 5 minutes. It will buy you 3 additional months of Aloha-workarounds. Just put Messages & Alerts on the Home-Page-Layout, go to Home-Page-Components, open Messages & Alerts there and add something like this in the text-box:
/1402932484000 is a timestamp, which can also be omitted or any other number can be used.
Also I wouldn't blame just us on this. For us, who used this, we did this with tears in our eyes - not with fun. The Aloha-UI is just sooo low-fi that it simply isn't enough for some state-of-the-art solutions. Visualforce-overrides or entire custom UIs come also with massive trade-offs. The workarounds were last, desperate measures where we simply could not deliver hi-fi UIs based on Aloha. Now the Lightning Experience UI should make most of the use-cases obsolete. Unfortunately we can't use LE immediately in all Orgs where necessary and even Spring'16 is too soon to let us switch all those Orgs to LE smoothly and without disruptions.
So I have no problems with the fact of the shutdown of Aloha-UI workarounds at all, but I would have been very happy if Salesforce had adjusted the shutdown-speed to the time they need to deliver a fully featured Lightning-Experience UI. We, also, need some time and without LE the was no smart way to deliver.
Anyway, if anyone at Salesforce is reading this: a little bit more time would be cool and I'm sure we all will happily throw these hacks in the trash where they belong.
You could also try to setup a community for some of your use cases. Injection of JS there is very simple via Footer or Header HTML when you customize the community UI. Even if you go with standard salesforce licenses and features, you could redirect some processes to a community UI where I could not find strong restrictions.