If you are using a npn/pnp transistor you can wire up the electrodes such that the collector-base and emitter-base capacitances are in parallel with each other, which will increase your capacitance/area factor.
For most single or douple poly bipolar structures, there usually exists a monosilicon/oxide/nitride/polysilicon(base) stack up. You can use the monosilicon as the positive electrode and the polysilicon as the negative electrode. You will want to use a deep collector and buried layer implants for your positive electrode such that you minimize the series resistance of that electrode.
Depending on the technology, some bipolar technologies do have double poly capacitors and MIM caps too.