For cost reasons (~$50 vs $200) I'm probably going to buy a 4 way KVM switch with a DSUB video connection for the mostly headless computers I have running for various purposes. The only concern I have is how quickly display port will kill off DVI; and with it the ability to fall back on an analog output.
In short: you'll be able to use an analogue VGA KVM for years to come.
To cut a short story long:
Given how long it has taken for DVI/HDMI to do away with a pure analogue VGA port (i.e. it hasn't yet - many cards still come with a DSUB port and those that don't carry the analogue signal on the DVI port so a DVI->DSUB adaptor can be used) I suspect it will be at least a couple of years before DVI fades away, and until DVI fades I assume that the analogue signals will still be present on most (if not all) DVI outputs.
Even if all new cards suddenly stop supporting analogue monitors (directly with a DSUB output or via DVI->DSUB) tomorrow you will be able to get VGA capable cards second hand for some years to come. The same goes for if all new monitors were to stop having VGA inputs tomorrow too.
The decision between PS/2 style mini-DIN keyboard/mouse connectors or USB connectors may be more of an issue, though not overly so. As well as many (most?) new portable devices coming with no old-style keyboard/mouse ports, many small-form PCs (like Acer's Revo) don't either and I've seen full-size desktops without them too, so those old ports are on the way out. I suspect the old keyboard/mouse connectors will be long gone before DSUB VGA connections are.