I built a capacitive liquid level sensor that works great as a main interference receiver
I'm about to rebuild it using a lower impedance design with ground isolation - if only I had known before...
USB isn't isolated. I wonder how many Arduino users know that. A desktop computer ground is connected to mains ground, a laptop running from a plug pack isn't.
Being connected to a PC ground isn't at all doom for a product. Your cellphone will be able to receive signals that are 10 pico watts in power while connected to your computer. I routinely build circuits where in the input signal is just 200uV and it sits a few inches away from a 125 MHz FPGA, DDR and 480Mbps USB2.0 chip.
Do you actually care if you are ground referenced? If you need a ground, you might as well use the PC ground. If you don't need a ground (because you need to float to measure something) then you will generally use an isolated DCDC part to generate the other supply and then let that float.
On your schematics, anything sensitive connect to analog ground. Any thing with square waves, connect it to digital ground. Use a DCDC for logic if you wish, but you SHOULD use an LDO for the analog. In fact, you might cascade two LDO. This is because the PSRR of an LDO at frequencies of interest might be just 70-80 dB, and if you are wanting to take a small signal and gain it up significantly, you will very quickly be at the limit of the PSRR spec.
So, say you have 5V coming in the from the USB. That will be 4.75V worst case. Use a 200 mV dropout LDO to get to 4.5V, and then another 200 mV dropout LDO to get to 4.3V. That 4.3V signal will be pristine. Use that for the opamps. If you need a negative, use a DCDC and follow that with an LDO.
And then tie the Analog and Digital grounds together at ONLY ONE PLACE with some 0603 or 0805 resistors. Usually, the one place will be the USB connector. But there are times where you might find it is better to tie them together elsewhere. You just have to experiment and find the sweet spot.
PS. The reason a cellphone can work so well when connected to a noisy ground is because it doesn't care that the ground is boucning all over the place. As the ground moves up, the 2.75V supply moves up. As the ground moves down, the 2.75V supply moves down.