If your issue isn't listed below, consult the Build documentation. There are some useful little pieces of information scattered throughout the build docs.
Z axis binding
If you remove the belt you can tell if one of the Z drive screws is more restricted than the other by feel.
Measure that your Z drive screws are parallel to each other. The X bar measurements in the spec make them a little longer than may be ideal. You may have to loosen the 2 x-bar-clamp-m4 on the motor end and slide the assembly containing the x-vert-drive-nut-trap toward the center of the machine. The x-motor-bracket-spacer does not fill the gap between the bracket (to which the motor is bolted) and the next assembly.
The x axis needs to be level once it's sitting on the Z screws. If your machine is on a (near) level surface, placing a spirit level on the extruder carriage will help you get the x axis close to correct.
The belt may not have sufficient clearance. If there are issues with the printed parts you may need an additional M4 washer or two with the idler bearings for the Z belt. The belt may be incorrectly routed.
Nuts may not be seated correctly in the x-vert-drive-nut traps.
Check the Z screw for grit and/or paint (usually nearer the ends, but it can happen elsewhere).
Note: the sockets that connect the z-drive screws to the motor shafts can have a weak hold on the motor shafts. This can be avoided by replacing the tubing covering the motor drive shaft to improve friction. Friction could also be improved by having a single plate with four holes on either side of the socket, as opposed to having four washers for the four screws.
Some 608 bearings may bind when the washers are placed either side. You might try using a nut directly on the bearing instead.
Some 8mm washers are too big (diameter). The 8mm washer then catches on the 4mm washers that hold the bearing in place as the Z screw turns. If necessary, you may remove the 8mm washers (as above), use different washers (15.8mm or smaller diameter seems to work), or mechanically adjust the 4mm washers (trim or file off a piece of the washer).
Washers can dig into the clamps the hold the Z screws when they are tightened. Putting a plate down in-between the washers and the clamp by prevent this.
Extrude Hole Position
How do I move the extrude hole in RepRap host software? The software thinks it's on the right side and mine is on the left.
You need to add some settings for your build platform to the file - <Your Home Directory>/.reprap/reprap.properties
replacing 5, 5 with the coordinates where you want the extruder to purge before printing.
How much "wobble" is there on the tip of your nozzle? Place your hand palm-upwards, put the tip of your finger over the nozzle hole, and press firmly upwards, but not too hard. Move your hand and finger around in the X & Y direction, applying some sideways force to the nozzle tip. Does it move around? Does your X carriage wobble in either direction (i.e., bearings move away from rods)? Try applying more or less force upwards through your finger while repeating it, and see if that affects it.
Y Axis Binding
The Y-belt bearing/washer combo at the very front of your Mendel Y belt —which has "a big washer" on it to constrain the belt from falling off the bearing— may actually be putting too much friction to your belt. (i.e., the side of the belt rubs on the side of the big washer). Lubrication, and/or a tiny bend in the washer reduces friction here.
Are your belts too tight, causing the carriage or bearings to bind on direction changes?
Are your belts too loose, causing backlash?
Check that the belts are not damaged (i.e., no missing teeth, teeth are consistently-spaced). Note that the supporting wires in a belt can break over time, leading to slipping.
X-Carriage Bearing Alignment
To test for this issue, disconnect the X belt entirely and make sure that the x-carriage rolls easily with gravity when you tip the Mendel.
Your electronics may be losing steps because motor signals are being sent "too fast." To isolate this issue, try disabling micro-stepping entirely and see if steps are still lost.
Remove power from your axes (turn off the machine) and gently push the X-carriage and Y-bed-carriage through their full motion, feeling for any changes in resistance throughout the motion. If resistance seems uneven, try removing the belt and see if it still occurs. If not, the printed cog on the motor is probably being eccentric.
You can see the results of (fairly large) backlash in these photos: http://picasaweb.google.com/themumbys/ScrewyCircles (In this particular case, a very stretchy belt was causing backlash. Steel wires in the belt are supposed to keep it from stretching.)
Strange behaviour of electronics, resets, etc.
A running RepRap can cause some quite interesting inductive and EM effects. Any open cabling can become an antenna for surrounding equipment (e.g., dremels, etc.), and this can potentially cause the electronics to get confused. To reduce the impact of this, you should put ferrite beads on all your motor leads. Also consider putting your electronics into a shielded box. Make sure you use known good cables for the USB connection. Ferrite cores help here too.
Sometimes the controls move motors in the wrong direction. This can often be fixed by flipping around the cables in the Arduino port that sends the commands.