I'd consider making a trip to Alexandria Union Station; this station is served by Amtrak and VRE and is adjacent to the King Street Metro station. The station is small but attractive-looking, and it is next to the truly impressive Washington Masonic Memorial. Use the Metro Yellow Line to get out there; you get to ride on the bridge over the Potomac River, which gives you some nice views of DC.
If you are going to go to Baltimore, you might as well use the Penn Line in one direction and the Camden Line in the other direction. To get from the Penn Line to the Camden Line, take the Baltimore light rail shuttle from Penn Station to the Mount Royal/University of Baltimore stop (or walk over there; it is less than a 5 minute walk from Penn Station). Then take the light rail south to the Camden Yards stop, which is on the opposite side of the warehouse outside of Oriole Park at Camden Yards. (Obviously you do the reverse if you use the Camden Line traveling to Baltimore.) You'll get to experience the annoyance of the light rail's on-street running with no signal preemption on the west side of downtown Baltimore (Howard Street). The light rail runs through a still-struggling part of Baltimore, especially in the northern part of downtown. This rail line connects with the Baltimore Metro Subway at the Lexington Market stations for both lines; the connection is neither obvious nor well-marked. From the light rail the subway station is one short block to the west.
In addition to what I noted above, there are a couple other locations of potential interest along/near the light rail segment you could use between Penn Station and Camden Station. At the aforementioned Mount Royal light rail station, you can see the north access to the important Howard Street tunnel. Down near Camden Station is M&T Bank Stadium (or as I like to call it, the Big Purple Playpen), home of the Baltimore Ravens. The stadium is adjacent to the next station south from Camden Yards on the light rail, Hamburg Street (not to mention across the parking lot from OPACY). Both the light rail and the Camden Line run next to the stadium.
Baltimore Penn Station itself is surprisingly small for such an important station; it is nowhere near as large as Washington Union Station, Philadelphia 30th Street Station, or Chicago Union Station (the last of which I got to see for the first time a couple weeks ago). The architecture is nice though. It is moderately similar to and somewhat larger than the Lancaster train station some 60 miles to the north-northeast. The station has a newsstand, a restaurant/bar, and a couple other small-scale amenities. From a train line perspective, the neatest thing about the station is you may have the opportunity to see an Amtrak Acela or Regional, a MARC train, and the light rail shuttle at the station at the same time. To get the best view of this, use the light rail shuttle and walk down to the far end of the platform. The light rail track is the one closest to the station's main lobby. You can also view some trains from outside the station along St. Paul Street (street east of the station); there are shields blocking part of the view but if you walk far enough north on the street, you can look down at the through tracks/trains at the station. Finally, one of the nicer, more arty neighborhoods in Baltimore, Mount Vernon, is immediately south of the station on the other side of Interstate 83 (that road is in a cut and not a barrier to north-south movement). Don't venture too far north of the station though; you'll enter one of the many rough parts of Baltimore.
Back to Washington, if you are a sports fan, two other things to check out that are rail-related are A) the Orange/Blue Line's descent from elevated to subway just outside RFK Stadium (you cannot miss the stadium, the lines approach the stadium from the northeast and then curve to the left, going underground to the stadium's west just before you reach the stadium) and B) the Washington Nationals' new ballpark being built near the Green Line Navy Yard station. The ballpark itself is a couple blocks south of the station.
2009 Phillies/Yankees World Series - aka the Acela Series