Depends on what ship you're trying to jam everything into, how long your planning on being out for and what you intend to get up to.
I find the
Krait MkII works best for me. Good jump range, SLF capable, excellent SC maneuverability.
SLF: are usually much faster than an exploration vessel so they get used for all the stoopid stuff (canyons, etc). They are also much more expendable than the mother ship (mine has 6 SLFs so its not a real hassle if I plant one into a canyon wall). Since most of the riskier flying is done in the SLF, you're less likely to need a Repair Limpet for your mother ship - saves 2 module slots.
Heatsinks: rarely used but if you jump into a nest of stars you'll wish you had one. Lightweight mod means you should take one as it has very little impact on jump range.
Multiple AFMUs: not really necessary unless you plan on being out for a year. My build has a second, but only as a weightless damage sponge. Never used it.
Cargo space: you can only synthesis 4 limpets at a time, so a size 2 rack makes sense if you're carrying any limpet controllers. Maybe a larger corrosion resistant rack if you plan on collecting xeno samples
Mining laser: only useful if you desperately need materials. If you have an SRV, then the laser is kinda redundant. You can't add a lightweight mod, so mining lasers can bite into your jump range. Not sure why my build has one, never used.
Plasma slug rail gun: useful for dumping fuel if you need extra range. Rarely used.
Chaff: celebratory fireworks!
Fuel transfer & repair limpet controllers: useful if your on an expedition with others who smack into things or forget to fuel up
Supercruise assist: stops you from kissing the sun accidentally while the fight scene is playing on your movie (exploration can be dull at times, best spiced with some viewing pleasure). Also neat for automated planetary orbit for gratuitous selfies.
Guardian visits: chuck on a point defense and a lighweight laser if you plan on visiting Guardian sites on your travels.