I pretty much stopped caring about this show after mid-season three, though I tuned back in occasionally. These are basically just my favorite slash stories from the glory days of S2--unlikely that I'll be adding to this page.
Sea Change by Yahtzee. Angel/Lindsey set right before S3. I totally believe that this actually happened.
Latency by Shrift. Gunn/Wes with glasses.
Comfortable by Shrift. Who makes a lot of the early S3 blunders hurt a lot less.
A Question of Style by Jane and Te. The old "this'll only sting a little" routine. Mmmm.