Hmm. This is going to be a tough pick. I'll sleep on it.
Thoughts on the entries-
1st Bracket - Lots of railgun-centric craft this bracket.
Urd's Swan - The main strength of this entry is the paintjob, using fades between shades of blue with a layer of very dark blue on top. It reminds me of the movie Tron.
Stardriven - A diagonal build. Very straight-line-y.The paintjob is interesting in how the white almost shadows the yellow. The thrusters blend in nicely. However, the reactors in the middle of the paintjob disrupt it.
Ewr - Another diagonal ship. The purple compliments the shields well. The ship is asymmetrical because of the control room, but it's not immediately obvious.
Phantom - This ship creates an interesting effect by making the high decals the same color as the base paint, allowing for patterns that would otherwise be impossible. I checked, and it still looks pretty good even with a variety of colors.
Splinter - This ship has an asymmetrical paintjob, with the colors not quite swapped. I feel as if it could utilize it's base color more then it does.
Outlaw - An asymmetrical ship, built around a railgun. It's nice how the crew color was changed to better blend in with the paint. The black gradients give it a sense of depth.
Industrial Mass Driver - There appears to be an error. Someone has accidentally submitted a Starsector ship. Joking aside, this has a very nice use of gradients, only broken up by the components. The The rail gun blends in well with the paint. The thrusters, however, are a tad jarring against the dark and pale grays.
Trident - My own entry. Very similar to Urd's Swan in design, with two engine rooms, two closely packed railguns, and four shields (I submitted it first, for the record). Is blue and white instead of blue and black. This ship tries to disguise a boxy design by adding slopes of armor and having a semi-chaotic paintjob.
2nd Bracket - Shame Jungle didn't get in. I had hopes for it. There are a lot of diagonal ships this bracket.
H4XXOR - Nice shape and good use of white to outline it. I like how the design changes from geometric straight lines to curves without any dissonance.
Goose - The black doesn't contrast very well with the slightly lighter black, leaving the main source of contrast between the yellow and the black/black. While other ships use this to draw attention to their shape, this just feels random. I'm not a fan of the regularity of the back end; the flatness of the line of thrusters and the uniformity of the spikes.
Harbringer's Echo - I question the wisdom of having another ship named Harbringer. The long, thin pieces combined with the chunkier body bring to mind either an insect, or an electric guitar. I think the white is underutilized.
Vortex - The only asymmetrical ship of second bracket. It looks like a spiral. The speckling of reactors break up the paintjob with little attempt to accommodate them. The colors do not contrast very much, All being approximately the same brightness. There was an attempt to color the inner and outer sides with shades of blue.
Crystal Guardian - Similar in name to the Crystal Angel of last design contest, assumedly if it wins they shall fuse together into the Crystal Guardian Angel. I'm questioning the use of whole squares, as opposed to fades, used to give it texture. The outline brings to mind deep sea life.
Kovlier - A diagonal ship. It highlights its contours well with the light light blue while the less light blue gives it shape. I feel as if it should a smoother transition between the fragmentary tail pieces and the solid body.
Excalibur - Also diagonal. It also uses Ions. The sporadic use of yellow is jarring compared to the straight lines of dark gray.
Fragarach - The colors were chosen well. The pale yellow compliments the thrusters while the two more subtly different shades of blue give the design depth. The flak blends in well.
3rd Bracket
Iridium - Very monochrome, which makes the purple of the shields and green of the reactors all the more apparent. On the flip side, the missiles blend in very well.
Nausicca/Nausicaa XL - Sounds vaguely like a drink order. Reminds me of that movie with a princess and giant bugs. The ship is very geometric
Araphel the Everlasting - Uses the same principles as Urd's Swan, but with red and purple: the same colors as the ions and shields. I think that the spikes of structure on the end would look better as armor, but then the missile's wouldn't be able to get out.
Paramount - The name and color scheme bring to mind a mountain. The green of the reactors blends in with the teal. I find the straightness of the side panels off putting compared to the slopes of the rest of the design.
Geode - My entry. Crew quarters and missile launchers contrast with the paintjob, too many straight lines for an organic appearance. Flak blends in nicely, though.
Queen's Hive - An inspired attempt to make a ship out of hexagons, reminiscent of a beehive. It uses three shades of orange / yellow, but I don't think the low decals and the paintjob (the two shades of yellow) contrast as well as the orange and tellow.. On the bright side, the engines blend in very good. Unfortunately everything else does not. The regularity of the paintjob is broken up by the components.
Stygil - Very straight. The color scheme is interesting in how it uses two shades of cyan, something not obvious at first glance.
Vengeance Diagonal. The dark and light grey give it depth, but I'm questioning the inclusion of the straight, perpendicular lines on the sides. They cut across everything else.
Nagalia - This ship reminds me of the Pokemon 'Kyogre.' I forgot what it was called and googled 'pokemon that's red, white, blue, and looks like a whale' and it was the first result. The missiles break up the straight lines of the paintjob and silhouette. The small white lines with a blue outline are jarring, they are the only lines that break up a region of color.
Ragros - Very Interesting design with lots of curves yet having a boxy centerpiece. The coloring is desaturated compared to other entries, but it pulls it off.