I actually have a list of favorites that aren't mentioned here, so I'll add them in case you haven't seen one of them.
'
Et Lux Et Tenebris Lucet' by Enigmaticblue is an AU S6 in which Spike saves Dawn and Buffy but is paralyzed in his fall from Glory's tower. It's amazing.
Slaymesoftly's 'Loves Lost' series goes AU sometime around 'Innocence', and features Buffy and Spike working together after she is captured by Angelus and Ethan Rayne. The first two parts, set in S2, have Spike still paralyzed after the events of 'What's My Line'. The first story is called '
Loves Lost'; the second is '
Love Awakened'. There are two more pieces, set in S3.
Slaymesoftly also has a between-the-lines, pre-Spuffy oneshot set in S2 called '
Later'. I love it so much I've made it head-canon.
Three more BTL S2 shorts are '
Equal Opportunities' by Constance (generic S2), '
Heartless' by foxinator (set around Valentine's Day), and '
Last Dance' by Darkrivertempest (set during 'Killed By Death'). There's also rabid1st's '
Nights in White Cotton' (again, set during 'Killed By Death').
perletwo's '
Burn It All Away' series is an AU collection with Spuffy romance much earlier than it happened in canon. The first few feature Spike while he's still in the wheelchair.
If you're ok with WIPs, tempestt has an AU showing how Dawn's presence could have drastically altered the series. It's getting regularly updated over on Elysian Fields and is called '
Remember When'.
Lastly, there's Enchantress's '
Crippled', in which Buffy takes Spike in after she paralyzes him during the beating at the end of 'Dead Things'.