Actually I think the mods here, like pretty much anywhere are so personalised that it's hard to get a coherent view of what might be a 'standard' set of upgrade.
I've only been around a few weeks, but I've started to get a feel for things and I think this may be a good starting point:
1) **EDITED** Add a filament dust remover and a filament guide of some sort
Thingiverse: http://www.thingiverse.com/search?q=fil … st&sa=
Thingiverse: http://www.thingiverse.com/search?q=sol … de&sa= (I like my own clip-on design best, but I am biased)
2) Build an enclosure
3) Upgrade your bed to glass or ceramic, this may require modifying the adjustment screws and possibly making some clips.
Thread: http://www.soliforum.com/topic/160/glass-bed/
4)Cable management, either a 'cable snake' or a clip on guide for the frame.
5) Add a filament 'wiper' to clear the nozzle before a print job starts
6) Upgrade your Z axis with M5 rod, this is getting more advanced and will require disassembly of the Z-Axis and purchase of assorted parts. (a definitive guide with parts list and suppliers in different countries would be great)
7) Upgrade your print head bracket to an ABS one, I believe it's called Lawsy's Mk5.
8) Print replacement parts for the X and Y carriage, again, this requires a teardown and confidence that you can rebuild it.
Thread: http://www.soliforum.com/topic/2813/pri … -consumer/
9) Add a fan to your extruder to cool printed plastic.
Thread: http://www.soliforum.com/topic/3045/mk5 … -consumer/
10) Add fans to your stepper motors
11) Replace your HotEnd, possibly with an all metal one that can print different materials at higher temps
12) Upgrade your Power Suppliy
13) Change your electronics
I'm sure there are others, and this list needs some more links, but IMHO these should all have their own stickies. If there are better guides than thos I list, or other specific mods, please add them here and I'll update this post.
Useful things:
a) You may also like to get a Pressure Gauge and build a mount for it for bed levelling, this is more of a tool than a mod.