General Tips

Research beforehand to understand which trains allow bikes, how many, in what form, etc
Be polite and follow the conductor's directions
Make sure you can maneuver your bike and bags independently; conductors may not be allowed to help
Consider one-way routes that start with transit and end at your house (or your car, or a very reliable/frequent form of transit like the subway); this gets travel logistics out of the way so you can enjoy your ride without worrying about a precise schedule to meet your train home

Amtrak General Tips

Full bike policy: https://www.amtrak.com/bring-your-bicycle-onboard
Bike service varies by line, only some stations accept bikes
Bikes require a reservation and a $20 charge per travel segment
The official max tire width is 2”, but slightly larger tires are generally fine and can be deflated if necessary (I have traveled dozens of times with a 2.25” tire, but you will be turned away with a fat bike)
There is no definitive, updated list of stations that accept bikes; the most reliable way to determine whether a station accepts bikes is to attempt a future booking to see whether the Amtrak website would let you reserve space for a bicycle (no need to input credit card or complete the booking)

Amtrak Carry-On Bicycle Service (Northeast Regional, Vermonter, etc):

You will carry your bike on to the train and store your bike in the designated hanging bike racks (blog post with photos of the typical situation)
Be prepared to carry your bike up several steep stairs to board train (not all stations have level boarding)
You can see/access to your bike while the train is moving
If bike rack is occupied by luggage, wait for a conductor to clear the space; your bike reservation gives you priority over any luggage blocking the bike rack
Be prepared to remove the front wheel; you might also need to lower the seatpost for larger frame sizes
Always carry straps (voile, bungees, or similar) in case they are necessary to secure your bike; don’t count on the provided Amtrak straps being present and in good condition

Amtrak Trainside Checked Bicycle Service (Floridian, Crescent, etc):

You will typically hand your bike up to a crew member who will store it in the baggage car, but you may also be asked to leave your bike trainside for crew members to load
At larger stations (e.g., Union Station DC), you might be required to check in at the counter and receive a bike luggage tag before boarding (at smaller unstaffed stations this is not required)
You will not be able to see or access your bike while the train is moving
Plan what to carry on the train and what to leave on your bike

Bags that don’t protrude from frame (e.g., frame and top tube bags) can generally stay on, but be prepared to quickly remove other bags (e.g., panniers) as necessary
Consider a small packable backpack to carry on to the train (a trash bag can also work)

At some stations, trains stop twice (once for coach, once for baggage and sleeper cars); your bike might be loaded/unloaded from the platform at one stop while you board/disembark at the other stop. Speak to a conductor for guidance.

MARC (Maryland regional rail)

Full bike policy: https://www.mta.maryland.gov/MARCbikes
Bikes allowed on all trains, no reservations required, no extra fee
Be aware that certain lines (e.g., Brunswick) only operate weekdays in the primary commuter direction
If too many people attempt to board a train with bikes, some might be turned away (but I haven’t heard firsthand of this happening)
Always carry straps (voile, bungees, or similar) to secure your bike if the train doesn’t have formal bike racks; people have been turned away without them!
Be prepared to carry your bike up several steep stairs to board train (not all stations have level boarding)

WMATA (DC Metro)

Full bike policy: https://wmata.com/service/bikes/guidelines.cfm
No reservations required, no extra fee, extensive service 7 days a week
Other than extremely limited exceptions (e.g., presidential inauguration), bikes are allowed at all times
All stations/trains are ADA-accessible; use elevators to enter/exit stations
Board at the front/back (not middle) of any train car; you’ll typically have the most space if you choose the front of first train car or back of the last train car.