NOTE: I personally hate both but thought others may enjoy!
1.Scully at least has a name; Riker gets a number, Chekote just a "Mister"
2.Mulder's boss named "Skinner", Picard's "Starfleet"
3.Mulder has been fired more times than all the "Star Trek" captains combined
4.As far as sub-plots go, Picard's holodeck trouble and Janeway's "Quest for Coffee" pale in comparison to the "Government-putting- LSD-in-my-water" thing.
5."Star Trek" aliens likely to try to steal / blow up your starship or misuse some alien artifact nobody's ever heard of before... "X-File" aliens likely to land their spaceship in your back yard, impregnate your dog for laughs, and walk off with your sister for twenty years...
6. EDITED OUT
7.Mulder not affected by the "I'm the captain, where did my shirt go?" disease like our friend, Mr. Kirk
8.Mulder looks better in a trenchcoat, even on the holodeck
9.Mulder's voice doesn't quaver when he threatens someone
10."Star Trek" captains all have hobbies; Mulder has obsessions
11.Helpless victims on "X-Files" not clearly identifiable by shirt color
12."Star Trek" captains have friends with names like 'Spock,' 'Neelix," or 'Data'...Mulder has friends with names like 'Deep Throat,' 'Mr. X', and 'The Lone Gunmen.
13.Mulder's gun doesn't look like a keychain
14.When Mulder shoots someone, they fall down and bleed respectably, not just glow and then disappear
15.When Mulder spouts physics, it actually makes sense
16."Star Trek" captains can't drive a stick
17.David Duchovny never cut a pop album
18.Mulder has never met God; if he did, he'd have a better question to ask than "Why does GOD need a STARSHIP?"
19.Before Kirk, Shatner wore a suit on "The Twilight Zone"... Before Picard, Stewart wore leather on "Dune"... Before Mulder, Duchovny wore a full length silk gown on "Twin Peaks" and showed his naked tushie in "The Rapture"
20.When Picard's brother died, he got misty eyed... When Sisko's wife died, he got depressed -- for about a week... When the hit man killed Mulder's dad, he got the crap beat out of him by Mulder
21.Nobody ever called Picard "Spooky" back at the Academy
22.If Mulder had an idol, it wouldn't be Ray Walston as the Academy groundskeeper
23.Mulder has better hair, even WITH Shatner's toupe
24.When the Borg stole Picard, they gave him a blank stare, a new name, and a laser light. When the aliens abducted Scully, they got her pregnant in 10 seconds flat; which proves, if nothing else, that "X-Files" must have better cast parties
25.At the close of the 2nd season, Mulder was trapped inside a buried refer car in New Mexico with a helicopter full of Marines led by Cancerman dropping satchel charges on his head, all the while trying to figure out why smallpox vaccinated ET corpses were there in the first place and what that had to do with Navajo encrypted DOD files that his dad wrote and what was Scully's name doing on them....At the end of last season, Janeway was wandering around the universe, lost without any way of getting 'Voyager' home... At the end of last season, Sisko was wandering around the station, lost without a plot...